From 0fb1df050a2ae1787da42a8c34b071fc44d76567 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Thu, 12 Sep 2024 19:31:47 +0000 Subject: [PATCH] Updating anvil-edge README for edge-24-09-12-18-17-1 --- reports/anvil-edge/README.md | 2 +- reports/anvil-edge/tool-tests/chunks.json | 10 +- .../edge-24-09-12-18-17-1/chunk.json | 7 + .../edge-24-09-12-18-17-1/chunk.txt | 24 + .../errors/168c5019d723e181.json | 45 + .../errors/2ad1970214efc1f1.json | 59 + .../errors/3c9b9a9b19ed1b5d.json | 57 + .../errors/6bc47c51ca0fac40.json | 45 + .../errors/73e4ef2f2e01965c.json | 55 + .../errors/7f37eb8a83e8664d.json | 57 + .../errors/87f976abf7756231.json | 45 + .../errors/8cda8a57308ec27c.json | 45 + .../errors/8e563efc628e146c.json | 45 + .../errors/8ee84a3a48b550c8.json | 45 + .../errors/9b3ec3f1f110d3c4.json | 82 ++ .../errors/a187d2dbacce08b7.json | 45 + .../errors/a555483f8adf0b56.json | 104 ++ .../errors/aff42d3d4ee95ab5.json | 57 + .../errors/d35b1c9b91227c0a.json | 45 + .../errors/de61d63a05be4330.json | 45 + .../edge-24-09-12-18-17-1/job-metrics.csv | 198 ++++ .../tool-tests/edge-24-09-12-18-17-1/jobs.txt | 197 ++++ .../edge-24-09-12-18-17-1/results.html | 291 +++++ .../edge-24-09-12-18-17-1/results.json | 1 + .../edge-24-09-12-18-17-1/results.xunit | 1020 +++++++++++++++++ .../edge-24-09-12-18-17-1/tools.yml | 126 ++ 26 files changed, 2746 insertions(+), 6 deletions(-) create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/chunk.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/chunk.txt create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/168c5019d723e181.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/2ad1970214efc1f1.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/3c9b9a9b19ed1b5d.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/6bc47c51ca0fac40.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/73e4ef2f2e01965c.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/7f37eb8a83e8664d.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/87f976abf7756231.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8cda8a57308ec27c.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8e563efc628e146c.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8ee84a3a48b550c8.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/9b3ec3f1f110d3c4.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/a187d2dbacce08b7.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/a555483f8adf0b56.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/aff42d3d4ee95ab5.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/d35b1c9b91227c0a.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/de61d63a05be4330.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/job-metrics.csv create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/jobs.txt create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.html create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.xunit create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/tools.yml diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index f1612903a..def11e9cb 100644 --- a/reports/anvil-edge/README.md +++ b/reports/anvil-edge/README.md @@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the Latest tool tests for each chunk: -
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 09 06:26:24 2024Mon Sep 02 06:26:43 2024
1ToolsetMon Sep 09 18:31:59 2024Mon Sep 02 18:31:49 2024
2ToolsetTue Sep 10 06:27:04 2024Tue Sep 03 06:25:36 2024
3ToolsetTue Sep 10 18:32:07 2024Tue Sep 03 18:31:25 2024
4ToolsetWed Sep 11 06:26:47 2024Wed Aug 28 06:26:28 2024
5ToolsetWed Sep 11 18:32:01 2024Wed Sep 04 18:30:27 2024
6ToolsetThu Sep 12 06:26:50 2024Thu Sep 05 06:27:04 2024
7ToolsetThu Sep 05 18:31:37 2024Thu Aug 29 18:32:00 2024
8ToolsetFri Sep 06 06:26:22 2024Fri Aug 30 06:25:36 2024
9ToolsetFri Sep 06 18:31:23 2024Fri Aug 30 18:31:41 2024
10ToolsetSat Sep 07 06:24:24 2024Sat Aug 31 06:24:40 2024
11ToolsetSat Sep 07 18:29:55 2024Sat Aug 31 18:29:37 2024
12ToolsetSun Sep 08 06:24:59 2024Sun Sep 01 06:26:20 2024
13ToolsetSun Sep 08 18:31:42 2024Sun Sep 01 18:29:57 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 09 06:26:24 2024Mon Sep 02 06:26:43 2024
1ToolsetMon Sep 09 18:31:59 2024Mon Sep 02 18:31:49 2024
2ToolsetTue Sep 10 06:27:04 2024Tue Sep 03 06:25:36 2024
3ToolsetTue Sep 10 18:32:07 2024Tue Sep 03 18:31:25 2024
4ToolsetWed Sep 11 06:26:47 2024Wed Aug 28 06:26:28 2024
5ToolsetWed Sep 11 18:32:01 2024Wed Sep 04 18:30:27 2024
6ToolsetThu Sep 12 06:26:50 2024Thu Sep 05 06:27:04 2024
7ToolsetThu Sep 12 18:33:11 2024Thu Sep 05 18:31:37 2024
8ToolsetFri Sep 06 06:26:22 2024Fri Aug 30 06:25:36 2024
9ToolsetFri Sep 06 18:31:23 2024Fri Aug 30 18:31:41 2024
10ToolsetSat Sep 07 06:24:24 2024Sat Aug 31 06:24:40 2024
11ToolsetSat Sep 07 18:29:55 2024Sat Aug 31 18:29:37 2024
12ToolsetSun Sep 08 06:24:59 2024Sun Sep 01 06:26:20 2024
13ToolsetSun Sep 08 18:31:42 2024Sun Sep 01 18:29:57 2024
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index e374815ce..b8902c163 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -42,11 +42,11 @@ "date2": "Thu Sep 05 06:27:04 2024" }, "7": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-05-18-15-1/results.html", - "date1": "Thu Sep 05 18:31:37 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-05-18-15-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-29-18-16-1/results.html", - "date2": "Thu Aug 29 18:32:00 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.html", + "date1": "Thu Sep 12 18:33:11 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-05-18-15-1/results.html", + "date2": "Thu Sep 05 18:31:37 2024" }, "8": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-06-06-11-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/chunk.json new file mode 100644 index 000000000..b1507b53c --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/chunk.json @@ -0,0 +1,7 @@ +{ + "7": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.html", + "date1": "Thu Sep 12 18:33:11 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/chunk.txt new file mode 100644 index 000000000..ec7eb31b6 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/chunk.txt @@ -0,0 +1,24 @@ +-t collection_element_identifiers --tool-version d3c07d270a50 +-t deeptools_plot_correlation --tool-version 32e451def88c +-t flash --tool-version a27654fc4270 +-t volcanoplot --tool-version 73b8cb5bddcd +-t medaka_variant --tool-version 43815fa60f3a +-t poretools_times --tool-version 960be5e0b47e +-t sailfish --tool-version a8f343909c17 +-t samtools_phase --tool-version b5c3b1856370 +-t samtools_phase --tool-version 1e5880498f52 +-t samtools_mpileup --tool-version fa7ad9b89f4a +-t anndata_import --tool-version 55e35e9203cf +-t anndata_import --tool-version fb9e030ffae4 +-t raceid_inspecttrajectory --tool-version c8434a623268 +-t raceid_inspecttrajectory --tool-version df8e4e54d367 +-t scanpy_normalize --tool-version ab55fe8030b6 +-t scanpy_scale_data --tool-version 9664a6c00fd1 +-t scanpy_scale_data --tool-version c6e52529260e +-t regex_find_replace --tool-version ae8c4b2488e7 +-t lofreq_call --tool-version e1461b5c52a0 +-t bcftools_plugin_fixploidy --tool-version 365325116147 +-t bcftools_stats --tool-version b17394940c7a +-t vcf2tsv --tool-version 285060661b45 +-t vcfhethom --tool-version 8254e0fe7358 +-t snpeff_sars_cov_2 --tool-version 2a3a00c1fa0a diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/168c5019d723e181.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/168c5019d723e181.json new file mode 100644 index 000000000..d6e8f33fc --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/168c5019d723e181.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "168c5019d723e181", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T18:54:22.925011", + "update_time": "2024-09-12T18:54:34.894706", + "galaxy_version": "24.1", + "external_id": "gxy-mrl6v", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/75/registry.xml' '/galaxy/server/database/jobs_directory/000/75/upload_params.json' '115:/galaxy/server/database/objects/b/a/9/dataset_ba944c94-4c23-4cb2-b583-438bad477192_files:/galaxy/server/database/objects/b/a/9/dataset_ba944c94-4c23-4cb2-b583-438bad477192.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_f53d6ek4\"", + "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"mpileup.1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_vnsldwr3\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"bam\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "f489600111a88594", + "src": "hda", + "uuid": "ba944c94-4c23-4cb2-b583-438bad477192" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/2ad1970214efc1f1.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/2ad1970214efc1f1.json new file mode 100644 index 000000000..b2ea970bb --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/2ad1970214efc1f1.json @@ -0,0 +1,59 @@ +{ + "model_class": "Job", + "id": "2ad1970214efc1f1", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy3", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T19:10:15.173436", + "update_time": "2024-09-12T19:10:35.166467", + "galaxy_version": "24.1", + "external_id": "gxy-g74vv", + "handler": null, + "job_runner_name": null, + "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/a6821f856a1e/raceid_inspecttrajectory/scripts/trajectoryinspect.R' '/galaxy/server/database/jobs_directory/000/134/configs/tmphxv6x5b_' 2> '/galaxy/server/database/objects/7/3/4/dataset_7349095f-5024-4676-bbc7-54bd70cc2b2d.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "trjfid": "{\"basic\": {\"__current_case__\": 1, \"cellsfromz\": \"3,9,2\", \"doit\": \"yes\", \"som\": {\"__current_case__\": 1, \"doit\": \"yes\", \"title\": \"Title\", \"use\": {\"__current_case__\": 0, \"def\": \"yes\"}, \"use_genes\": {\"__current_case__\": 0, \"typer\": \"genelist\", \"use_genes\": \"Clca4,Mki67,Defa24,Ybx1,Vasp,Apoa1\"}, \"use_types\": \"\\\\\\\\_\\\\\\\\d+\"}, \"use\": {\"__current_case__\": 1, \"def\": \"no\", \"filterset_minexpr\": \"1\", \"filterset_minnumber\": \"2\", \"getsom_alpha\": \"0.5\", \"getsom_nb\": \"1000\", \"plotheat_xgrid\": false, \"plotheat_xlab\": false, \"plotheat_ygrid\": true, \"procsom_corthr\": \"0.5\", \"procsom_minsom\": \"5\"}}}", + "trjsid": "{\"basic\": {\"__current_case__\": 1, \"br\": \"6,5,3\", \"doit\": \"yes\", \"i\": \"5\", \"use\": {\"__current_case__\": 1, \"def\": \"no\", \"ndiffgenes\": \"14\", \"zscore\": true}}}" + }, + "inputs": { + "inputrds": { + "id": "81d018ec229ef1c2", + "src": "hda", + "uuid": "fe43bdf3-5177-45e3-9926-e17393153f0b" + } + }, + "outputs": { + "outpdf": { + "id": "663a32c8d74e11b0", + "src": "hda", + "uuid": "d54ab71e-75c6-46ee-8649-ecf57d24cf03" + }, + "outdiffgenes": { + "id": "64f324641a66e464", + "src": "hda", + "uuid": "22218adb-5292-411f-b25d-e7fc28bfa5fc" + }, + "outlog": { + "id": "731a0f6c2e09e1b3", + "src": "hda", + "uuid": "7349095f-5024-4676-bbc7-54bd70cc2b2d" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "NULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\nNULL\nNULL\nNULL\nnull device \n 1 \n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "NULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\nNULL\nNULL\nNULL\nnull device \n 1 \n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/3c9b9a9b19ed1b5d.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/3c9b9a9b19ed1b5d.json new file mode 100644 index 000000000..7d0c312af --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/3c9b9a9b19ed1b5d.json @@ -0,0 +1,57 @@ +{ + "model_class": "Job", + "id": "3c9b9a9b19ed1b5d", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T19:20:00.208909", + "update_time": "2024-09-12T19:20:14.171223", + "galaxy_version": "24.1", + "external_id": "gxy-96x7v", + "handler": null, + "job_runner_name": null, + "command_line": "ln -s '/galaxy/server/database/objects/2/e/f/dataset_2efde3d5-4472-4a87-8ac7-b7632b2f7ae8.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/b/2/4/dataset_b24dbd0f-6326-451b-8e67-3caac826cba8.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/0/f/6/metadata_0f6bc320-32d1-42ce-8213-fe7581a6f465.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", + "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", + "variant_types": "\"\"", + "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", + "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 218, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}" + }, + "inputs": { + "reference_source|ref": { + "id": "7299715a3323e0c8", + "src": "hda", + "uuid": "2efde3d5-4472-4a87-8ac7-b7632b2f7ae8" + }, + "reads": { + "id": "097c9c86ae789649", + "src": "hda", + "uuid": "b24dbd0f-6326-451b-8e67-3caac826cba8" + } + }, + "outputs": { + "variants": { + "id": "cebde5ad27a14bc1", + "src": "hda", + "uuid": "8e2a573c-380f-45b3-bd7e-39628de603c4" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "INFO [2024-09-12 19:20:07,645]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 19:20:07,656]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:20:09,439]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/159/tmp/lofreq2_call_parallel3do47ktx/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "INFO [2024-09-12 19:20:07,645]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 19:20:07,656]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:20:09,439]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/159/tmp/lofreq2_call_parallel3do47ktx/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/6bc47c51ca0fac40.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/6bc47c51ca0fac40.json new file mode 100644 index 000000000..56e7742d1 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/6bc47c51ca0fac40.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "6bc47c51ca0fac40", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T18:40:26.813204", + "update_time": "2024-09-12T18:40:39.694520", + "galaxy_version": "24.1", + "external_id": "gxy-dh55v", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/24/registry.xml' '/galaxy/server/database/jobs_directory/000/24/upload_params.json' '46:/galaxy/server/database/objects/4/1/9/dataset_419b779c-07f0-4435-bf5c-7904f2ad0a3a_files:/galaxy/server/database/objects/4/1/9/dataset_419b779c-07f0-4435-bf5c-7904f2ad0a3a.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_ctqvtdoj\"", + "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"input.tab\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_m58m3k0v\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"tabular\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "47d8f1eb9c871c1f", + "src": "hda", + "uuid": "419b779c-07f0-4435-bf5c-7904f2ad0a3a" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/73e4ef2f2e01965c.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/73e4ef2f2e01965c.json new file mode 100644 index 000000000..187e1b59b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/73e4ef2f2e01965c.json @@ -0,0 +1,55 @@ +{ + "model_class": "Job", + "id": "73e4ef2f2e01965c", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T19:26:40.846878", + "update_time": "2024-09-12T19:26:45.740636", + "galaxy_version": "24.1", + "external_id": "gxy-kkhjl", + "handler": null, + "job_runner_name": null, + "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/4/3/dataset_8435d287-38fb-4227-8d9f-8d005c03e930.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/0/e/8/dataset_0e87e6a5-9e28-4f76-9090-0931695f266f.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools stats --regions-overlap 1 input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/2/3/c/dataset_23c6ce8b-ff0e-4dce-bc53-28f0d930e12c.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "plot_title": "\"\"", + "sec_default": "{\"af_tag\": \"\", \"afbins\": {\"__current_case__\": 0, \"afbins_select\": \"default\"}, \"depth\": {\"__current_case__\": 0, \"set_depth\": \"no\"}, \"exons_file\": null, \"first_allele_only\": false, \"reference_source\": {\"__current_case__\": 0, \"reference_source_selector\": \"\"}, \"split_by_ID\": false, \"user_tstv\": \"\", \"verbose\": false}", + "sec_restrict": "{\"apply_filters\": \"\", \"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}" + }, + "inputs": { + "input_file": { + "id": "1df47cc768d658ae", + "src": "hda", + "uuid": "8435d287-38fb-4227-8d9f-8d005c03e930" + }, + "inputB_file": { + "id": "36650d18141ad1f9", + "src": "hda", + "uuid": "0e87e6a5-9e28-4f76-9090-0931695f266f" + } + }, + "outputs": { + "output_file": { + "id": "f40a8c5d0662968d", + "src": "hda", + "uuid": "23c6ce8b-ff0e-4dce-bc53-28f0d930e12c" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/7f37eb8a83e8664d.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/7f37eb8a83e8664d.json new file mode 100644 index 000000000..da997bc55 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/7f37eb8a83e8664d.json @@ -0,0 +1,57 @@ +{ + "model_class": "Job", + "id": "7f37eb8a83e8664d", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T18:39:10.628994", + "update_time": "2024-09-12T18:39:40.437808", + "galaxy_version": "24.1", + "external_id": "gxy-q5frh", + "handler": null, + "job_runner_name": null, + "command_line": "Rscript '/galaxy/server/database/jobs_directory/000/20/configs/tmp843q3dhl'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "out_options": "{\"rscript_out\": false}", + "plot_options": "{\"boxes\": false, \"legend\": null, \"legend_labs\": \"Down,Not Sig,Up\", \"title\": null, \"xlab\": null, \"xmax\": \"\", \"xmin\": \"\", \"ylab\": null, \"ymax\": \"\"}", + "labels": "{\"__current_case__\": 2, \"label_select\": \"none\"}", + "lfc_thresh": "\"0.0\"", + "signif_thresh": "\"0.05\"", + "label_col": "\"1\"", + "lfc_col": "\"2\"", + "pval_col": "\"3\"", + "fdr_col": "\"4\"", + "header": "\"auto\"" + }, + "inputs": { + "input": { + "id": "133051a93011d0ef", + "src": "hda", + "uuid": "680e9f2b-3bdc-46fb-8ffe-6caa685fc759" + } + }, + "outputs": { + "plot": { + "id": "fbfc0c3850803a3c", + "src": "hda", + "uuid": "b141f9c5-eb57-4588-b315-40739b472c02" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "[1] \"Header row detected\"\nnull device \n 1 \nR version 4.0.5 (2021-03-31)\nPlatform: x86_64-conda-linux-gnu (64-bit)\nRunning under: Debian GNU/Linux 10 (buster)\n\nMatrix products: default\nBLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.15.so\n\nlocale:\n [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 \n [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 \n [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C \n[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C \n\nattached base packages:\n[1] stats graphics grDevices utils datasets methods base \n\nother attached packages:\n[1] ggrepel_0.9.1 ggplot2_3.3.3 dplyr_1.0.6 \n\nloaded via a namespace (and not attached):\n [1] Rcpp_1.0.6 magrittr_2.0.1 tidyselect_1.1.1 munsell_0.5.0 \n [5] colorspace_2.0-1 R6_2.5.0 rlang_0.4.11 fansi_0.5.0 \n [9] grid_4.0.5 gtable_0.3.0 utf8_1.2.1 withr_2.4.2 \n[13] ellipsis_0.3.2 digest_0.6.27 tibble_3.1.2 lifecycle_1.0.0 \n[17] crayon_1.4.1 purrr_0.3.4 farver_2.1.0 vctrs_0.3.8 \n[21] glue_1.4.2 labeling_0.4.2 compiler_4.0.5 pillar_1.6.1 \n[25] generics_0.1.0 scales_1.1.1 pkgconfig_2.0.3 \n", + "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "[1] \"Header row detected\"\nnull device \n 1 \nR version 4.0.5 (2021-03-31)\nPlatform: x86_64-conda-linux-gnu (64-bit)\nRunning under: Debian GNU/Linux 10 (buster)\n\nMatrix products: default\nBLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.15.so\n\nlocale:\n [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 \n [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 \n [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C \n[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C \n\nattached base packages:\n[1] stats graphics grDevices utils datasets methods base \n\nother attached packages:\n[1] ggrepel_0.9.1 ggplot2_3.3.3 dplyr_1.0.6 \n\nloaded via a namespace (and not attached):\n [1] Rcpp_1.0.6 magrittr_2.0.1 tidyselect_1.1.1 munsell_0.5.0 \n [5] colorspace_2.0-1 R6_2.5.0 rlang_0.4.11 fansi_0.5.0 \n [9] grid_4.0.5 gtable_0.3.0 utf8_1.2.1 withr_2.4.2 \n[13] ellipsis_0.3.2 digest_0.6.27 tibble_3.1.2 lifecycle_1.0.0 \n[17] crayon_1.4.1 purrr_0.3.4 farver_2.1.0 vctrs_0.3.8 \n[21] glue_1.4.2 labeling_0.4.2 compiler_4.0.5 pillar_1.6.1 \n[25] generics_0.1.0 scales_1.1.1 pkgconfig_2.0.3 \n", + "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/87f976abf7756231.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/87f976abf7756231.json new file mode 100644 index 000000000..91f7e3134 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/87f976abf7756231.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "87f976abf7756231", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T19:01:08.940221", + "update_time": "2024-09-12T19:01:21.417206", + "galaxy_version": "24.1", + "external_id": "gxy-6rjf7", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/103/registry.xml' '/galaxy/server/database/jobs_directory/000/103/upload_params.json' '143:/galaxy/server/database/objects/7/0/f/dataset_70fb857a-ea4a-4cb5-9250-985dd5794dc9_files:/galaxy/server/database/objects/7/0/f/dataset_70fb857a-ea4a-4cb5-9250-985dd5794dc9.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_x8gv6a1l\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"firstlayer.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_lxluy5no\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "27b3bc9031b124c5", + "src": "hda", + "uuid": "70fb857a-ea4a-4cb5-9250-985dd5794dc9" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8cda8a57308ec27c.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8cda8a57308ec27c.json new file mode 100644 index 000000000..f7f91bbf2 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8cda8a57308ec27c.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "8cda8a57308ec27c", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T19:02:06.920982", + "update_time": "2024-09-12T19:02:19.580217", + "galaxy_version": "24.1", + "external_id": "gxy-lnpjx", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/109/registry.xml' '/galaxy/server/database/jobs_directory/000/109/upload_params.json' '149:/galaxy/server/database/objects/e/1/7/dataset_e17cc87c-ba81-429c-9a04-7132d5e74dae_files:/galaxy/server/database/objects/e/1/7/dataset_e17cc87c-ba81-429c-9a04-7132d5e74dae.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_7kwzpmmu\"", + "files_metadata": "{\"__current_case__\": 111, \"file_type\": \"loom\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"krumsiek11.loom\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_de0stpf5\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"loom\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "37420a6232681e35", + "src": "hda", + "uuid": "e17cc87c-ba81-429c-9a04-7132d5e74dae" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8e563efc628e146c.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8e563efc628e146c.json new file mode 100644 index 000000000..7adfe8675 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8e563efc628e146c.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "8e563efc628e146c", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T18:57:56.063064", + "update_time": "2024-09-12T18:58:07.558515", + "galaxy_version": "24.1", + "external_id": "gxy-ttf4l", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/94/registry.xml' '/galaxy/server/database/jobs_directory/000/94/upload_params.json' '134:/galaxy/server/database/objects/1/8/7/dataset_187367f0-1619-423c-967c-61d8ffdddbbe_files:/galaxy/server/database/objects/1/8/7/dataset_187367f0-1619-423c-967c-61d8ffdddbbe.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_q_tbgwtn\"", + "files_metadata": "{\"__current_case__\": 111, \"file_type\": \"loom\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"krumsiek11.loom\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_m7u4xuhi\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"loom\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "2ad1970214efc1f1", + "src": "hda", + "uuid": "187367f0-1619-423c-967c-61d8ffdddbbe" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8ee84a3a48b550c8.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8ee84a3a48b550c8.json new file mode 100644 index 000000000..7fa24f323 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/8ee84a3a48b550c8.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "8ee84a3a48b550c8", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T18:37:55.889914", + "update_time": "2024-09-12T18:38:08.130906", + "galaxy_version": "24.1", + "external_id": "gxy-6wfsx", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/14/registry.xml' '/galaxy/server/database/jobs_directory/000/14/upload_params.json' '32:/galaxy/server/database/objects/5/4/2/dataset_5427b566-65ae-4fe7-ba89-69c63adc580c_files:/galaxy/server/database/objects/5/4/2/dataset_5427b566-65ae-4fe7-ba89-69c63adc580c.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_uue1c7pg\"", + "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"flash_forward_in4.fastqsanger.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ad5jizs8\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "072067071fcb9cc1", + "src": "hda", + "uuid": "5427b566-65ae-4fe7-ba89-69c63adc580c" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/9b3ec3f1f110d3c4.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/9b3ec3f1f110d3c4.json new file mode 100644 index 000000000..82d5293df --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/9b3ec3f1f110d3c4.json @@ -0,0 +1,82 @@ +{ + "model_class": "Job", + "id": "9b3ec3f1f110d3c4", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T18:48:54.088211", + "update_time": "2024-09-12T18:48:59.647494", + "galaxy_version": "24.1", + "external_id": "gxy-hdlsq", + "handler": null, + "job_runner_name": null, + "command_line": "sailfish index --transcripts /galaxy/server/database/objects/3/4/9/dataset_3494bf84-f97b-49e7-98a5-8789e9f8d5bc.dat --kmerSize 21 --out ./index_dir --threads \"${GALAXY_SLOTS:-4}\" && ln -s /galaxy/server/database/objects/6/1/6/dataset_616dd9f5-0f3b-42b2-9491-7b78b6283fee.dat ./mate1.fastq && ln -s /galaxy/server/database/objects/9/f/f/dataset_9ff10746-bcea-4d0e-b556-3bd5e22b6e1c.dat ./mate2.fastq && sailfish quant --index ./index_dir --mates1 <(zcat ./mate1.fastq) --mates2 <(zcat ./mate2.fastq) --libType \"IU\" --output ./results --threads \"${GALAXY_SLOTS:-4}\" --gcSizeSamp 1 --gcSpeedSamp 1 --fldMean 200 --fldSD 80 --maxReadOcc 200 --maxFragLen 1000 --txpAggregationKey 'gene_id' --numBiasSamples 1000000 --numFragSamples 10000 --numGibbsSamples 0 --numBootstraps 0", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fasta\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "numBootstraps": "\"0\"", + "numGibbsSamples": "\"0\"", + "numFragSamples": "\"10000\"", + "numBiasSamples": "\"1000000\"", + "allowDovetail": "false", + "enforceLibCompat": "false", + "ignoreLibCompat": "false", + "txpAggregationKey": "\"gene_id\"", + "maxFragLen": "\"1000\"", + "unsmoothedFLD": "false", + "discardOrphans": "false", + "useVBOpt": "false", + "noEffectiveLengthCorrection": "false", + "maxReadOcc": "\"200\"", + "fldSD": "\"80\"", + "fldMean": "\"200\"", + "strictIntersect": "false", + "gcSpeedSamp": "\"1\"", + "gcSizeSamp": "\"1\"", + "dumpEq": "false", + "gcBiasCorrect": "false", + "biasCorrect": "false", + "geneMap": null, + "single_or_paired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 76, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 77, \"src\": \"hda\"}]}, \"orientation\": \"I\", \"single_or_paired_opts\": \"paired\", \"strandedness\": \"U\"}", + "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"kmerSize\": \"21\", \"ownFile\": {\"values\": [{\"id\": 75, \"src\": \"hda\"}]}}" + }, + "inputs": { + "refTranscriptSource|ownFile": { + "id": "168c5019d723e181", + "src": "hda", + "uuid": "3494bf84-f97b-49e7-98a5-8789e9f8d5bc" + }, + "single_or_paired|input_mate1": { + "id": "d35b1c9b91227c0a", + "src": "hda", + "uuid": "616dd9f5-0f3b-42b2-9491-7b78b6283fee" + }, + "single_or_paired|input_mate2": { + "id": "6f2c1b5a12d2a732", + "src": "hda", + "uuid": "9ff10746-bcea-4d0e-b556-3bd5e22b6e1c" + } + }, + "outputs": { + "output_quant": { + "id": "4c335ad89d24fbaa", + "src": "hda", + "uuid": "0cf1dc2f-2051-4722-9ea2-00d8c9e388a0" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.00110978s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 3.7451e-05s\nWriting sequence data to file . . . done\nElapsed time: 6.5654e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000113315s\ndone\nElapsed time: 0.00327229s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00145451s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { /dev/fd/63 }\n# [ mates2 ] => { /dev/fd/62 }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:48:56.748] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:48:56.842] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:48:56.843] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:48:56.843] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:48:56.843] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:48:56.843] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:48:56.843] [stderrLog] [info] Done loading index\n\n[2024-09-12 18:48:56.839] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:48:56.843] [jointLog] [info] done\n[2024-09-12 18:48:56.864] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:48:56.864] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:48:56.865] [jointLog] [info] Estimating effective lengths\nDone Quasi-Mapping \n\n[2024-09-12 18:48:56.875] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:48:56.875] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:48:56.875] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:48:56.876] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 64 | max rel diff. = 0.00117687\n[2024-09-12 18:48:56.876] [jointLog] [info] Finished optimizer\n[2024-09-12 18:48:56.876] [jointLog] [info] writing output \n\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.00110978s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 3.7451e-05s\nWriting sequence data to file . . . done\nElapsed time: 6.5654e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000113315s\ndone\nElapsed time: 0.00327229s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00145451s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { /dev/fd/63 }\n# [ mates2 ] => { /dev/fd/62 }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:48:56.748] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:48:56.842] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:48:56.843] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:48:56.843] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:48:56.843] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:48:56.843] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:48:56.843] [stderrLog] [info] Done loading index\n\n[2024-09-12 18:48:56.839] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:48:56.843] [jointLog] [info] done\n[2024-09-12 18:48:56.864] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:48:56.864] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:48:56.865] [jointLog] [info] Estimating effective lengths\nDone Quasi-Mapping \n\n[2024-09-12 18:48:56.875] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:48:56.875] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:48:56.875] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:48:56.876] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 64 | max rel diff. = 0.00117687\n[2024-09-12 18:48:56.876] [jointLog] [info] Finished optimizer\n[2024-09-12 18:48:56.876] [jointLog] [info] writing output \n\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/a187d2dbacce08b7.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/a187d2dbacce08b7.json new file mode 100644 index 000000000..eb309726a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/a187d2dbacce08b7.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "a187d2dbacce08b7", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T19:30:45.917464", + "update_time": "2024-09-12T19:30:57.621944", + "galaxy_version": "24.1", + "external_id": "gxy-skdtz", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/197/registry.xml' '/galaxy/server/database/jobs_directory/000/197/upload_params.json' '258:/galaxy/server/database/objects/e/0/7/dataset_e07d7e89-86da-4aa8-bef6-0fd201884a76_files:/galaxy/server/database/objects/e/0/7/dataset_e07d7e89-86da-4aa8-bef6-0fd201884a76.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_xn0gfz27\"", + "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"input.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_cxq95v1b\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"vcf\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "f01f0898a078319b", + "src": "hda", + "uuid": "e07d7e89-86da-4aa8-bef6-0fd201884a76" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/a555483f8adf0b56.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/a555483f8adf0b56.json new file mode 100644 index 000000000..f1d24dfdd --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/a555483f8adf0b56.json @@ -0,0 +1,104 @@ +{ + "model_class": "Job", + "id": "a555483f8adf0b56", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T18:37:06.183128", + "update_time": "2024-09-12T18:37:11.218680", + "galaxy_version": "24.1", + "external_id": "gxy-hx847", + "handler": null, + "job_runner_name": null, + "command_line": "flash --threads=${GALAXY_SLOTS:-1} -m 10 -M 65 -x 0.25 --allow-outies '/galaxy/server/database/objects/6/f/2/dataset_6f29742b-f7cf-4fa7-bd72-c8061fb7201b.dat' '/galaxy/server/database/objects/4/2/b/dataset_42b41e9e-6b98-4208-b561-97fad08a9f3a.dat' -p 33 --output-suffix='' > '/galaxy/server/database/objects/d/2/7/dataset_d27feeb6-177f-4504-885b-94a6631771ec.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "save_log": "true", + "generate_histogram": "true", + "allow_outies": "true", + "max_mismatch_density": "\"0.25\"", + "max_overlap": "\"65\"", + "min_overlap": "\"10\"", + "layout": "{\"__current_case__\": 0, \"forward\": {\"values\": [{\"id\": 13, \"src\": \"hda\"}]}, \"reverse\": {\"values\": [{\"id\": 14, \"src\": \"hda\"}]}, \"select_layout\": \"individual\"}" + }, + "inputs": { + "layout|forward": { + "id": "fb532b15014e4bc3", + "src": "hda", + "uuid": "6f29742b-f7cf-4fa7-bd72-c8061fb7201b" + }, + "layout|reverse": { + "id": "8ee84a3a48b550c8", + "src": "hda", + "uuid": "42b41e9e-6b98-4208-b561-97fad08a9f3a" + } + }, + "outputs": { + "merged_paired_reads": { + "id": "5d8b72ff95536eda", + "src": "hda", + "uuid": "8fea43c1-5922-42a1-a62e-e4c236f56e95" + }, + "unmerged_paired_reads_f": { + "id": "685638cbe319d87b", + "src": "hda", + "uuid": "bbbc318d-c86d-4419-b82e-58bfd51271b9" + }, + "unmerged_paired_reads_r": { + "id": "020136fbd4bcb69e", + "src": "hda", + "uuid": "32ce73e9-2974-44e7-812e-c635bc703ba0" + }, + "hist": { + "id": "084d2fbcfb1378fe", + "src": "hda", + "uuid": "8c64cbc3-eb27-4343-aacd-9f4a8f897846" + }, + "log": { + "id": "c5e3b73e1038c55a", + "src": "hda", + "uuid": "d27feeb6-177f-4504-885b-94a6631771ec" + }, + "histogram": { + "id": "7f37eb8a83e8664d", + "src": "hda", + "uuid": "94d55b20-996e-432b-abbd-f914ab168dbc" + }, + "hist_in": { + "id": "bd8048b02cf14b1b", + "src": "hda", + "uuid": "1053321e-fba9-4012-a065-6e4ede4575ee" + }, + "hist_out": { + "id": "b85f302f89048917", + "src": "hda", + "uuid": "76b3dde9-8a64-47f5-aa99-b98475309b6b" + }, + "histogram_in": { + "id": "accec78088c642c0", + "src": "hda", + "uuid": "2c7728b8-9949-48ed-b11b-0b2b2ce93e65" + }, + "histogram_out": { + "id": "6bc47c51ca0fac40", + "src": "hda", + "uuid": "d47843d9-b474-4c18-9934-748746a48472" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/aff42d3d4ee95ab5.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/aff42d3d4ee95ab5.json new file mode 100644 index 000000000..22e630dab --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/aff42d3d4ee95ab5.json @@ -0,0 +1,57 @@ +{ + "model_class": "Job", + "id": "aff42d3d4ee95ab5", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T19:22:52.190076", + "update_time": "2024-09-12T19:22:59.823447", + "galaxy_version": "24.1", + "external_id": "gxy-cnmcz", + "handler": null, + "job_runner_name": null, + "command_line": "ln -s '/galaxy/server/database/objects/3/8/c/dataset_38c16d84-ec4e-43bf-9b32-2702fb3a788d.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/3/4/1/dataset_341a5a5a-bd31-4651-8e5f-c7eb5659795a.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/1/6/0/metadata_1609f14d-df7d-467c-9de1-bc293594970f.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && ln -s variants.vcf variants.vcf.gz && gzip -df variants.vcf.gz && echo set_all_off", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "filter_control": "{\"__current_case__\": 0, \"bonf\": \"1\", \"filter_type\": \"set_all_off\", \"others\": \"--no-default-filter\", \"sig\": \"1\"}", + "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", + "variant_types": "\"--call-indels --only-indels\"", + "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", + "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 231, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}" + }, + "inputs": { + "reference_source|ref": { + "id": "e1812a2a3571e07b", + "src": "hda", + "uuid": "38c16d84-ec4e-43bf-9b32-2702fb3a788d" + }, + "reads": { + "id": "b691b770366e328d", + "src": "hda", + "uuid": "341a5a5a-bd31-4651-8e5f-c7eb5659795a" + } + }, + "outputs": { + "variants": { + "id": "80316208467124cb", + "src": "hda", + "uuid": "1792d2f5-6231-4256-b713-625b05d9ac18" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "INFO [2024-09-12 19:22:54,460]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2024-09-12 19:22:54,472]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 0\nNumber of indel tests performed: 9\nINFO [2024-09-12 19:22:57,118]: Copying concatenated vcf file to final destination\nset_all_off\n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "INFO [2024-09-12 19:22:54,460]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2024-09-12 19:22:54,472]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 0\nNumber of indel tests performed: 9\nINFO [2024-09-12 19:22:57,118]: Copying concatenated vcf file to final destination\nset_all_off\n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/d35b1c9b91227c0a.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/d35b1c9b91227c0a.json new file mode 100644 index 000000000..e2f932577 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/d35b1c9b91227c0a.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "d35b1c9b91227c0a", + "history_id": "7dbaf9c5b5117ca4", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-12T18:54:23.310213", + "update_time": "2024-09-12T18:54:36.332637", + "galaxy_version": "24.1", + "external_id": "gxy-s8mbw", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/76/registry.xml' '/galaxy/server/database/jobs_directory/000/76/upload_params.json' 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'/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/74/registry.xml' '/galaxy/server/database/jobs_directory/000/74/upload_params.json' '114:/galaxy/server/database/objects/7/1/c/dataset_71c116b5-d6f9-450b-bcac-75fb29865199_files:/galaxy/server/database/objects/7/1/c/dataset_71c116b5-d6f9-450b-bcac-75fb29865199.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_52xgosd9\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"samtools_phase_in_2.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_hrvuwb7o\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "f7d1576a38292913", + "src": "hda", + "uuid": "71c116b5-d6f9-450b-bcac-75fb29865199" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/job-metrics.csv b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/job-metrics.csv new file mode 100644 index 000000000..9ff4339b4 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/job-metrics.csv @@ -0,0 +1,198 @@ +id,history_id,history_name,state,tool_id,invocation_id,workflow_id,cpuacct.usage,galaxy_memory_mb,galaxy_slots,memory.limit_in_bytes,memory.peak,memory.soft_limit_in_bytes,memtotal,processor_count,runtime_seconds 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a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/jobs.txt b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/jobs.txt new file mode 100644 index 000000000..bef2163ab --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/jobs.txt @@ -0,0 +1,197 @@ +a187d2dbacce08b7 error 2024-09-12T19:30:57.621944 upload1 +6ad687e5d7de8a1e ok 2024-09-12T19:30:43.811990 toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0 +9a8ca9c8f7b2f5eb ok 2024-09-12T19:30:27.667541 upload1 +001c40e7415c60a4 ok 2024-09-12T19:30:05.221038 toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0 +f4a166451f5478d9 ok 2024-09-12T19:29:50.394293 upload1 +1e3af13e533eb89a ok 2024-09-12T19:29:27.667120 toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0 +47cac9c08ab275b7 ok 2024-09-12T19:29:12.494013 upload1 +82c07cc7b0ddf2de ok 2024-09-12T19:28:48.556846 toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0 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2024-09-12T19:24:15.358315 upload1 +323c7e8d4ee2b3fb ok 2024-09-12T19:24:15.257982 upload1 +e3507d56264a9dd3 ok 2024-09-12T19:23:50.337965 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4 +3c4080a7bf05a76e ok 2024-09-12T19:23:29.917210 upload1 +6acf16d205cb43e5 ok 2024-09-12T19:23:29.326568 upload1 +598ee9a3145b0971 ok 2024-09-12T19:23:29.226064 upload1 +aff42d3d4ee95ab5 error 2024-09-12T19:22:59.823447 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2 +dd8e0ee53546640e ok 2024-09-12T19:22:51.707055 upload1 +167f3b2097c06696 ok 2024-09-12T19:22:50.968010 upload1 +5c0ae45e23f6c784 ok 2024-09-12T19:22:26.611057 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2 +3bfe12de541ae942 ok 2024-09-12T19:22:09.131451 upload1 +139746bd725bd19c ok 2024-09-12T19:22:08.301105 upload1 +53fd8acef2b5620c ok 2024-09-12T19:21:44.049089 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2 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2024-09-12T19:09:50.967164 toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy3 +5a4b9b7bd08dc852 ok 2024-09-12T19:09:28.747446 upload1 +02fc949abb04889b ok 2024-09-12T19:09:05.592772 toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy3 +9aba506ac8551114 ok 2024-09-12T19:08:43.467049 upload1 +e965b9395c8197dd ok 2024-09-12T19:08:19.324849 toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy3 +d0d08e34d4ff0725 ok 2024-09-12T19:07:59.784462 upload1 +ff2ab0acd0bea7bb ok 2024-09-12T19:07:36.512177 toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy3 +5ad45bb156e2a7a4 ok 2024-09-12T19:06:56.103574 upload1 +6470afa683bc0ef9 ok 2024-09-12T19:06:30.890406 toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 +d141b75fa49a67c7 ok 2024-09-12T19:06:12.659482 upload1 +1164dd96f36d60ff ok 2024-09-12T19:05:50.556860 toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 +70b841ae0f47b03a ok 2024-09-12T19:05:33.590404 upload1 +f54ecdbe2e8a2f91 ok 2024-09-12T19:05:33.119369 upload1 +0a36ad0bce1b08d3 ok 2024-09-12T19:05:32.887879 upload1 +66a1e74d4479a401 ok 2024-09-12T19:05:31.708687 upload1 +c7107b466fd08f8b ok 2024-09-12T19:04:59.412951 toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 +91d185b0c8cb31e3 ok 2024-09-12T19:04:41.340359 upload1 +f489600111a88594 ok 2024-09-12T19:04:19.124373 toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 +f7d1576a38292913 ok 2024-09-12T19:04:01.959445 upload1 +e4aa0207225c348e ok 2024-09-12T19:03:38.700584 toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 +de86a819d0c290b6 ok 2024-09-12T19:03:21.825749 upload1 +5c1ddb477486569a ok 2024-09-12T19:02:58.271882 toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 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toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 +3976925a9227969f ok 2024-09-12T18:59:32.111800 upload1 +58061d892d57cfde ok 2024-09-12T18:59:08.770697 toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1 +f5dd1991fd210037 ok 2024-09-12T18:58:30.167513 upload1 +8e563efc628e146c error 2024-09-12T18:58:07.558515 upload1 +f2b001bafb7f1e18 ok 2024-09-12T18:57:53.599162 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7 +ca5c14a2636662ff ok 2024-09-12T18:57:38.039292 upload1 +addf2f2df9b554a8 ok 2024-09-12T18:57:37.884230 upload1 +34989088e8881d23 ok 2024-09-12T18:57:13.887547 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7 +d5891e03661115e3 ok 2024-09-12T18:56:59.228570 upload1 +0cf591c82edaee31 ok 2024-09-12T18:56:58.233974 upload1 +48068ee1e0edd97f ok 2024-09-12T18:56:35.427913 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7 +129531a63b7a5513 ok 2024-09-12T18:56:19.921050 upload1 +43691146cb9acd87 ok 2024-09-12T18:56:19.854368 upload1 +92087b09cfc8a7f1 ok 2024-09-12T18:55:55.668872 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7 +2e470f49e54464da ok 2024-09-12T18:55:41.265938 upload1 +2e3546eb0c2a0f11 ok 2024-09-12T18:55:40.463807 upload1 +f491a846e11318f6 ok 2024-09-12T18:55:17.345839 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7 +859213c2a6222ab9 ok 2024-09-12T18:54:58.641376 upload1 +07295b63630cd388 ok 2024-09-12T18:54:57.845067 upload1 +6f2c1b5a12d2a732 ok 2024-09-12T18:54:47.600957 upload1 +4c335ad89d24fbaa ok 2024-09-12T18:54:46.611758 upload1 +d35b1c9b91227c0a error 2024-09-12T18:54:36.332637 upload1 +168c5019d723e181 error 2024-09-12T18:54:34.894706 upload1 +de61d63a05be4330 error 2024-09-12T18:54:21.025592 upload1 +db95d19a8092a982 ok 2024-09-12T18:54:05.920877 toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2 +5b643a3584b3d2cc ok 2024-09-12T18:53:49.724275 upload1 +9d96d267d35b97f8 ok 2024-09-12T18:53:24.495565 toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2 +2cb04974f106202d ok 2024-09-12T18:53:08.293751 upload1 +93e63a590627fa02 ok 2024-09-12T18:52:42.309056 toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2 +90db6de268572cdc ok 2024-09-12T18:52:26.975390 upload1 +c217d4ee7c71fbe1 ok 2024-09-12T18:52:02.968648 toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2 +65d21c8dd103e196 ok 2024-09-12T18:51:47.648242 upload1 +adfc13cf15abc938 ok 2024-09-12T18:51:22.713107 toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2 +a6a56682b130fe7d ok 2024-09-12T18:51:04.152262 upload1 +3932b8f998703360 ok 2024-09-12T18:50:39.012948 toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1 +c044fbf4a85808aa ok 2024-09-12T18:50:21.354838 upload1 +5b47da6b838a28b9 ok 2024-09-12T18:50:21.227239 upload1 +38c6ecde7a68c98a ok 2024-09-12T18:50:20.574689 upload1 +dcc5df0733668a06 ok 2024-09-12T18:50:17.399861 upload1 +c7b1b9ca8b9b6fbc ok 2024-09-12T18:49:46.736156 toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1 +d569bffeb771697d ok 2024-09-12T18:49:29.167349 upload1 +d39b4356c0d01d30 ok 2024-09-12T18:49:28.388214 upload1 +095ab72dfe189fb3 ok 2024-09-12T18:49:27.187205 upload1 +9b3ec3f1f110d3c4 error 2024-09-12T18:48:59.647494 toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1 +008775b360117abf ok 2024-09-12T18:48:53.537468 upload1 +5c858a8da752f283 ok 2024-09-12T18:48:53.447867 upload1 +7e0d5152986e8835 ok 2024-09-12T18:48:52.459394 upload1 +5c9f142b579b34d2 ok 2024-09-12T18:48:24.865059 toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1 +2c586af689b790c8 ok 2024-09-12T18:47:57.868911 upload1 +ededad3470a5b941 ok 2024-09-12T18:47:56.963134 upload1 +ee28955812120d89 ok 2024-09-12T18:47:56.925302 upload1 +47d8f1eb9c871c1f ok 2024-09-12T18:47:27.304603 toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0 +8544f36ebf32bf8b ok 2024-09-12T18:47:11.339184 upload1 +cbbc4ddf6fc5a56d ok 2024-09-12T18:46:46.899106 toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0 +b921f920f2f0c5c5 ok 2024-09-12T18:46:30.887155 upload1 +fbfc0c3850803a3c ok 2024-09-12T18:46:07.541360 toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0 +133051a93011d0ef ok 2024-09-12T18:45:50.654867 upload1 +351dc77277b31b5b ok 2024-09-12T18:45:27.214221 toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0 +5911fd8579ff189d ok 2024-09-12T18:45:10.619200 upload1 +05264c584b20b27c ok 2024-09-12T18:44:46.912968 toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0 +cf0a14c93d5c0da4 ok 2024-09-12T18:44:05.604376 upload1 +4fc50e55ceaaf610 ok 2024-09-12T18:43:41.141077 toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1 +f535697429a960af ok 2024-09-12T18:43:22.554234 upload1 +4cb3c7cd46ca3b31 ok 2024-09-12T18:43:22.513671 upload1 +e5c0cb7b99d7758f ok 2024-09-12T18:42:58.621570 toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1 +072067071fcb9cc1 ok 2024-09-12T18:42:36.672506 upload1 +d472d3e2b25c7efe ok 2024-09-12T18:42:36.523986 upload1 +2c620e7ec978a081 ok 2024-09-12T18:42:34.992245 upload1 +84dfdb049c81a807 ok 2024-09-12T18:42:06.602834 toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1 +0e8df4f6392532d8 ok 2024-09-12T18:41:10.200157 upload1 +0f6192a68a5def8f ok 2024-09-12T18:41:08.625303 upload1 +e1a4aeccaf57fd0d ok 2024-09-12T18:41:08.501645 upload1 +d7c412a2f18e9b24 ok 2024-09-12T18:40:49.136138 upload1 +6bc47c51ca0fac40 error 2024-09-12T18:40:39.694520 upload1 +accec78088c642c0 ok 2024-09-12T18:40:25.533390 toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6 +bd8048b02cf14b1b ok 2024-09-12T18:40:03.949362 upload1 +b85f302f89048917 ok 2024-09-12T18:40:03.717429 upload1 +7f37eb8a83e8664d error 2024-09-12T18:39:40.437808 toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6 +c5e3b73e1038c55a ok 2024-09-12T18:39:10.400943 upload1 +084d2fbcfb1378fe ok 2024-09-12T18:38:45.045456 toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4 +020136fbd4bcb69e ok 2024-09-12T18:38:30.392237 upload1 +685638cbe319d87b ok 2024-09-12T18:38:30.337000 upload1 +5d8b72ff95536eda ok 2024-09-12T18:38:17.643146 upload1 +8ee84a3a48b550c8 error 2024-09-12T18:38:08.130906 upload1 +fb532b15014e4bc3 ok 2024-09-12T18:37:53.226759 toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4 +4be41249a61c6fc0 ok 2024-09-12T18:37:37.530597 upload1 +535909161eea3dd3 ok 2024-09-12T18:37:37.373847 upload1 +a555483f8adf0b56 error 2024-09-12T18:37:11.218680 toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4 +8d1ac837aaa7a2ff ok 2024-09-12T18:37:05.878028 upload1 +679fdd37d61da960 ok 2024-09-12T18:37:05.836800 upload1 +31cd6671df161099 ok 2024-09-12T18:36:40.081631 toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4 +acc30b44fe994885 ok 2024-09-12T18:36:22.374740 upload1 +8ebadddd0ec9ce8d ok 2024-09-12T18:36:22.224693 upload1 +4007dfbee97184dc ok 2024-09-12T18:35:57.248012 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0 +fb8cfd0ec3ddf688 ok 2024-09-12T18:35:38.090190 upload1 +d5bb8b6d17283723 ok 2024-09-12T18:35:14.568247 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0 +7dbaf9c5b5117ca4 ok 2024-09-12T18:34:13.569451 upload1 diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.html b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.html new file mode 100644 index 000000000..a004de815 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
+
+
+
+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.json b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.json new file mode 100644 index 000000000..a5da6be78 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 85, "errors": 12, "failures": 11, "skips": 1}, "tests": [{"id": "anndata_import/0.7.5+galaxy1-0", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 0, "time_seconds": 12.377711772918701, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "anndata_import/0.7.5+galaxy1-0", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 0, "time_seconds": 13.397853374481201, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "anndata_import/0.7.5+galaxy1-1", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 1, "time_seconds": 61.398624658584595, "inputs": {"hd5_format|in|input": {"src": "hda", "id": "00d3574f47297cd3"}, "hd5_format|in|first_column_names": true, "hd5_format|in|adata_format": "tabular"}, "job": {"model_class": "Job", "id": "58061d892d57cfde", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T18:58:30.377842", "update_time": "2024-09-12T18:59:08.770697", "galaxy_version": "24.1", "external_id": "gxy-78q68", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/96/configs/tmpv98bfgrs' && python '/galaxy/server/database/jobs_directory/000/96/configs/tmpv98bfgrs'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 1, \"adata_format\": \"tabular\", \"first_column_names\": true, \"input\": {\"values\": [{\"id\": 135, \"src\": \"hda\"}]}}}"}, "inputs": {"hd5_format|in|input": {"id": "00d3574f47297cd3", "src": "hda", "uuid": "a118dc7f-c3f1-4f94-977d-8d49094eb104"}}, "outputs": {"anndata": {"id": "b36cbbca30efa737", "src": "hda", "uuid": "afc22555-dadd-4f16-a00c-4ca145b1d9fa"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_csv(\n '/galaxy/server/database/objects/a/1/1/dataset_a118dc7f-c3f1-4f94-977d-8d49094eb104.dat',\n delimiter=',',\n first_column_names=True)\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_csv(\n '/galaxy/server/database/objects/a/1/1/dataset_a118dc7f-c3f1-4f94-977d-8d49094eb104.dat',\n delimiter=',',\n first_column_names=True)\n\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 18:58:50", "plugin": "core", "name": "end_epoch", "raw_value": "1726167530.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 18:58:49", "plugin": "core", "name": "start_epoch", "raw_value": "1726167529.0000000"}, {"title": "Memory Allocated (MB)", "value": "2147", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2147.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "anndata_import/0.7.5+galaxy1-1", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 1, "time_seconds": 39.18535089492798, "inputs": {"hd5_format|in|input": {"src": "hda", "id": "7164e81b0d7425b0"}, "hd5_format|in|first_column_names": true, "hd5_format|in|adata_format": "tabular"}, "job": {"model_class": "Job", "id": "5c1ddb477486569a", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:02:42.647360", "update_time": "2024-09-12T19:02:58.271882", "galaxy_version": "24.1", "external_id": "gxy-tfpjz", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/111/configs/tmp523xaoq0' && python '/galaxy/server/database/jobs_directory/000/111/configs/tmp523xaoq0'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 1, \"adata_format\": \"tabular\", \"first_column_names\": true, \"input\": {\"values\": [{\"id\": 150, \"src\": \"hda\"}]}}}"}, "inputs": {"hd5_format|in|input": {"id": "7164e81b0d7425b0", "src": "hda", "uuid": "a74294b1-ed12-4dfb-aa92-7674207acef1"}}, "outputs": {"anndata": {"id": "c800c30f096844a8", "src": "hda", "uuid": "b593d159-3bce-48bf-b051-651458715b70"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_csv(\n '/galaxy/server/database/objects/a/7/4/dataset_a74294b1-ed12-4dfb-aa92-7674207acef1.dat',\n delimiter=',',\n first_column_names=True)\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_csv(\n '/galaxy/server/database/objects/a/7/4/dataset_a74294b1-ed12-4dfb-aa92-7674207acef1.dat',\n delimiter=',',\n first_column_names=True)\n\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:02:46", "plugin": "core", "name": "end_epoch", "raw_value": "1726167766.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:02:44", "plugin": "core", "name": "start_epoch", "raw_value": "1726167764.0000000"}, {"title": "Memory Allocated (MB)", "value": "2147", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2147.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "anndata_import/0.7.5+galaxy1-2", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 2, "time_seconds": 41.57810163497925, "inputs": {"hd5_format|in|input": {"src": "hda", "id": "535baa9fce26ccae"}, "hd5_format|in|first_column_names": true, "hd5_format|in|adata_format": "tabular"}, "job": {"model_class": "Job", "id": "79020648f32f3ffe", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T18:59:32.556163", "update_time": "2024-09-12T18:59:50.332996", "galaxy_version": "24.1", "external_id": "gxy-tdpnz", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/98/configs/tmpwyb5gl7z' && python '/galaxy/server/database/jobs_directory/000/98/configs/tmpwyb5gl7z'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 1, \"adata_format\": \"tabular\", \"first_column_names\": true, \"input\": {\"values\": [{\"id\": 137, \"src\": \"hda\"}]}}}"}, "inputs": {"hd5_format|in|input": {"id": "535baa9fce26ccae", "src": "hda", "uuid": "0641aa4a-0ae1-465e-b7fe-53c6908c3ae4"}}, "outputs": {"anndata": {"id": "dd42a26499c3c416", "src": "hda", "uuid": "c7343399-ba13-43ee-87e5-35abc2232736"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_csv(\n '/galaxy/server/database/objects/0/6/4/dataset_0641aa4a-0ae1-465e-b7fe-53c6908c3ae4.dat',\n delimiter='\\t',\n first_column_names=True)\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_csv(\n '/galaxy/server/database/objects/0/6/4/dataset_0641aa4a-0ae1-465e-b7fe-53c6908c3ae4.dat',\n delimiter='\\t',\n first_column_names=True)\n\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 18:59:36", "plugin": "core", "name": "end_epoch", "raw_value": "1726167576.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 18:59:34", "plugin": "core", "name": "start_epoch", "raw_value": "1726167574.0000000"}, {"title": "Memory Allocated (MB)", "value": "2147", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2147.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "anndata_import/0.7.5+galaxy1-2", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 2, "time_seconds": 40.226635456085205, "inputs": {"hd5_format|in|input": {"src": "hda", "id": "016055815d296980"}, "hd5_format|in|first_column_names": true, "hd5_format|in|adata_format": "tabular"}, "job": {"model_class": "Job", "id": "e4aa0207225c348e", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:03:22.257756", "update_time": "2024-09-12T19:03:38.700584", "galaxy_version": "24.1", "external_id": "gxy-h7cxj", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/113/configs/tmppztsqcah' && python '/galaxy/server/database/jobs_directory/000/113/configs/tmppztsqcah'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 1, \"adata_format\": \"tabular\", \"first_column_names\": true, \"input\": {\"values\": [{\"id\": 152, \"src\": \"hda\"}]}}}"}, "inputs": {"hd5_format|in|input": {"id": "016055815d296980", "src": "hda", "uuid": "26bb0340-5009-48b1-9c49-9c13f2c5579e"}}, "outputs": {"anndata": {"id": "18fa148a5295dfb4", "src": "hda", "uuid": "1bd0580a-699e-4abf-b3d6-e8d539388724"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_csv(\n '/galaxy/server/database/objects/2/6/b/dataset_26bb0340-5009-48b1-9c49-9c13f2c5579e.dat',\n delimiter='\\t',\n first_column_names=True)\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_csv(\n '/galaxy/server/database/objects/2/6/b/dataset_26bb0340-5009-48b1-9c49-9c13f2c5579e.dat',\n delimiter='\\t',\n first_column_names=True)\n\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:03:25", "plugin": "core", "name": "end_epoch", "raw_value": "1726167805.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:03:23", "plugin": "core", "name": "start_epoch", "raw_value": "1726167803.0000000"}, {"title": "Memory Allocated (MB)", "value": "2147", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2147.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "anndata_import/0.7.5+galaxy1-3", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 3, "time_seconds": 39.2788360118866, "inputs": {"hd5_format|in|matrix": {"src": "hda", "id": "a27deddf8028d897"}, "hd5_format|in|tenx|use": "no", "hd5_format|in|adata_format": "mtx"}, "job": {"model_class": "Job", "id": "6b98ba1db45e9428", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:00:12.897221", "update_time": "2024-09-12T19:00:29.749689", "galaxy_version": "24.1", "external_id": "gxy-t4g4h", "handler": null, "job_runner_name": null, "command_line": "mkdir mtx && cat '/galaxy/server/database/jobs_directory/000/100/configs/tmpri0ey4cb' && python '/galaxy/server/database/jobs_directory/000/100/configs/tmpri0ey4cb' && rm -rf mtx", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 3, \"adata_format\": \"mtx\", \"matrix\": {\"values\": [{\"id\": 139, \"src\": \"hda\"}]}, \"tenx\": {\"__current_case__\": 0, \"use\": \"no\"}}}"}, "inputs": {"hd5_format|in|matrix": {"id": "a27deddf8028d897", "src": "hda", "uuid": "30385314-83b9-4e9a-b433-28e965f4d349"}}, "outputs": {"anndata": {"id": "cd32dd82950707d7", "src": "hda", "uuid": "c0e7e67c-c54f-4b15-a531-273ce6d8d28c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_mtx(filename='/galaxy/server/database/objects/3/0/3/dataset_30385314-83b9-4e9a-b433-28e965f4d349.dat')\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_mtx(filename='/galaxy/server/database/objects/3/0/3/dataset_30385314-83b9-4e9a-b433-28e965f4d349.dat')\n\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:00:16", "plugin": "core", "name": "end_epoch", "raw_value": "1726167616.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:00:14", "plugin": "core", "name": "start_epoch", "raw_value": "1726167614.0000000"}, {"title": "Memory Allocated (MB)", "value": "2147", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2147.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "anndata_import/0.7.5+galaxy1-3", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 3, "time_seconds": 40.492592573165894, "inputs": {"hd5_format|in|matrix": {"src": "hda", "id": "6a36c29e1ea63497"}, "hd5_format|in|tenx|use": "no", "hd5_format|in|adata_format": "mtx"}, "job": {"model_class": "Job", "id": "f489600111a88594", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:04:02.151404", "update_time": "2024-09-12T19:04:19.124373", "galaxy_version": "24.1", "external_id": "gxy-prlwv", "handler": null, "job_runner_name": null, "command_line": "mkdir mtx && cat '/galaxy/server/database/jobs_directory/000/115/configs/tmpuiqvktsb' && python '/galaxy/server/database/jobs_directory/000/115/configs/tmpuiqvktsb' && rm -rf mtx", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 3, \"adata_format\": \"mtx\", \"matrix\": {\"values\": [{\"id\": 154, \"src\": \"hda\"}]}, \"tenx\": {\"__current_case__\": 0, \"use\": \"no\"}}}"}, "inputs": {"hd5_format|in|matrix": {"id": "6a36c29e1ea63497", "src": "hda", "uuid": "8e20b4d9-37ef-4be1-9aec-123dd48b0730"}}, "outputs": {"anndata": {"id": "ec1a2c0a9eaa7b91", "src": "hda", "uuid": "e450af69-3f04-4197-bf29-7c58f8be53c1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_mtx(filename='/galaxy/server/database/objects/8/e/2/dataset_8e20b4d9-37ef-4be1-9aec-123dd48b0730.dat')\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_mtx(filename='/galaxy/server/database/objects/8/e/2/dataset_8e20b4d9-37ef-4be1-9aec-123dd48b0730.dat')\n\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:04:06", "plugin": "core", "name": "end_epoch", "raw_value": "1726167846.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:04:04", "plugin": "core", "name": "start_epoch", "raw_value": "1726167844.0000000"}, {"title": "Memory Allocated (MB)", "value": "2147", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2147.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "anndata_import/0.7.5+galaxy1-4", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 4, "time_seconds": 37.98934078216553, "inputs": {"hd5_format|in|input": {"src": "hda", "id": "7f3d1601c4009108"}, "hd5_format|in|adata_format": "umi_tools", "hd5_format|filetype": "anndata"}, "job": {"model_class": "Job", "id": "de1e0de05c234c72", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:00:52.267432", "update_time": "2024-09-12T19:01:07.960148", "galaxy_version": "24.1", "external_id": "gxy-snkff", "handler": null, "job_runner_name": null, "command_line": "gzip -c '/galaxy/server/database/objects/9/2/e/dataset_92e448a4-7eac-455b-acdd-c69852ab0e23.dat' > umi_tools_input.gz && cat '/galaxy/server/database/jobs_directory/000/102/configs/tmpmpknl153' && python '/galaxy/server/database/jobs_directory/000/102/configs/tmpmpknl153'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 4, \"adata_format\": \"umi_tools\", \"input\": {\"values\": [{\"id\": 141, \"src\": \"hda\"}]}}}"}, "inputs": {"hd5_format|in|input": {"id": "7f3d1601c4009108", "src": "hda", "uuid": "92e448a4-7eac-455b-acdd-c69852ab0e23"}}, "outputs": {"anndata": {"id": "9676c215d5c4dd43", "src": "hda", "uuid": "e7ac44b5-e898-46eb-bae7-8cc3d3f49106"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_umi_tools('umi_tools_input.gz')\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_umi_tools('umi_tools_input.gz')\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:00:55", "plugin": "core", "name": "end_epoch", "raw_value": "1726167655.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:00:53", "plugin": "core", "name": "start_epoch", "raw_value": "1726167653.0000000"}, {"title": "Memory Allocated (MB)", "value": "2147", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2147.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output anndata: different than expected, difference (using sim_size):\n( /tmp/tmp6qahdqpyimport.umi_tools.h5ad v. /tmp/tmpr2uk13v5import.umi_tools.h5ad )\nFiles /tmp/tmp6qahdqpyimport.umi_tools.h5ad=25320b but /tmp/tmpr2uk13v5import.umi_tools.h5ad=11048b - compare by size (delta=10000) failed"], "status": "failure"}}, {"id": "anndata_import/0.7.5+galaxy1-4", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 4, "time_seconds": 39.89377760887146, "inputs": {"hd5_format|in|input": {"src": "hda", "id": "1e7eb26eab8a29b7"}, "hd5_format|in|adata_format": "umi_tools", "hd5_format|filetype": "anndata"}, "job": {"model_class": "Job", "id": "c7107b466fd08f8b", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:04:41.720697", "update_time": "2024-09-12T19:04:59.412951", "galaxy_version": "24.1", "external_id": "gxy-ntqxs", "handler": null, "job_runner_name": null, "command_line": "gzip -c '/galaxy/server/database/objects/e/a/b/dataset_eabdbfd6-2ac3-46e7-8a50-054937900c9d.dat' > umi_tools_input.gz && cat '/galaxy/server/database/jobs_directory/000/117/configs/tmptoy46guf' && python '/galaxy/server/database/jobs_directory/000/117/configs/tmptoy46guf'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 4, \"adata_format\": \"umi_tools\", \"input\": {\"values\": [{\"id\": 156, \"src\": \"hda\"}]}}}"}, "inputs": {"hd5_format|in|input": {"id": "1e7eb26eab8a29b7", "src": "hda", "uuid": "eabdbfd6-2ac3-46e7-8a50-054937900c9d"}}, "outputs": {"anndata": {"id": "c6729a9807c00a1b", "src": "hda", "uuid": "88589127-7c94-4851-bc42-844da572266f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_umi_tools('umi_tools_input.gz')\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_umi_tools('umi_tools_input.gz')\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:04:46", "plugin": "core", "name": "end_epoch", "raw_value": "1726167886.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:04:44", "plugin": "core", "name": "start_epoch", "raw_value": "1726167884.0000000"}, {"title": "Memory Allocated (MB)", "value": "2147", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2147.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output anndata: different than expected, difference (using sim_size):\n( /tmp/tmpy_kiqh5jimport.umi_tools.h5ad v. /tmp/tmpsc1418wbimport.umi_tools.h5ad )\nFiles /tmp/tmpy_kiqh5jimport.umi_tools.h5ad=25320b but /tmp/tmpsc1418wbimport.umi_tools.h5ad=11048b - compare by size (delta=10000) failed"], "status": "failure"}}, {"id": "anndata_import/0.7.5+galaxy1-5", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 5, "time_seconds": 13.032787084579468, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "anndata_import/0.7.5+galaxy1-5", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 5, "time_seconds": 51.09281325340271, "inputs": {"hd5_format|mainmatrix": {"src": "hda", "id": "c6ce6f36f9563605"}, "hd5_format|other_files": {"src": "hda", "id": "3c9b9a9b19ed1b5d"}, "hd5_format|coldata": {"src": "hda", "id": "3c73dc41ba386e1d"}, "hd5_format|rowdata": {"src": "hda", "id": "4bccf3265d7b0025"}, "hd5_format|filetype": "loom"}, "job": {"model_class": "Job", "id": "1164dd96f36d60ff", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:05:33.858089", "update_time": "2024-09-12T19:05:50.556860", "galaxy_version": "24.1", "external_id": "gxy-n9w4b", "handler": null, "job_runner_name": null, "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/fb9e030ffae4/anndata_import/tsv_to_loompy.py' -c '/galaxy/server/database/objects/0/6/2/dataset_062cd24c-8fe5-4149-b440-00dd7a5bb06a.dat' -r '/galaxy/server/database/objects/8/a/2/dataset_8a26b23b-5d19-4376-9159-bd315ba0aa23.dat' -f '/galaxy/server/database/objects/4/7/c/dataset_47c5f49b-902c-43fd-ad05-8061c055d490.dat' '/galaxy/server/database/objects/b/e/1/dataset_be116685-ec1c-4e2c-94a7-24cb8c2016a8.dat'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 1, \"coldata\": {\"values\": [{\"id\": 160, \"src\": \"hda\"}]}, \"filetype\": \"loom\", \"mainmatrix\": {\"values\": [{\"id\": 158, \"src\": \"hda\"}]}, \"other_files\": {\"values\": [{\"id\": 159, \"src\": \"hda\"}]}, \"rowdata\": {\"values\": [{\"id\": 161, \"src\": \"hda\"}]}}"}, "inputs": {"hd5_format|mainmatrix": {"id": "c6ce6f36f9563605", "src": "hda", "uuid": "47c5f49b-902c-43fd-ad05-8061c055d490"}, "hd5_format|other_files": {"id": "3c9b9a9b19ed1b5d", "src": "hda", "uuid": "be116685-ec1c-4e2c-94a7-24cb8c2016a8"}, "hd5_format|other_files1": {"id": "3c9b9a9b19ed1b5d", "src": "hda", "uuid": "be116685-ec1c-4e2c-94a7-24cb8c2016a8"}, "hd5_format|coldata": {"id": "3c73dc41ba386e1d", "src": "hda", "uuid": "062cd24c-8fe5-4149-b440-00dd7a5bb06a"}, "hd5_format|rowdata": {"id": "4bccf3265d7b0025", "src": "hda", "uuid": "8a26b23b-5d19-4376-9159-bd315ba0aa23"}}, "outputs": {"loomdata": {"id": "3aac882fa0868af6", "src": "hda", "uuid": "812a0aa3-3b7e-4145-b64e-e5bec6d4aa95"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:05:37", "plugin": "core", "name": "end_epoch", "raw_value": "1726167937.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:05:35", "plugin": "core", "name": "start_epoch", "raw_value": "1726167935.0000000"}, {"title": "Memory Allocated (MB)", "value": "2147", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2147.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output loomdata: different than expected, difference (using sim_size):\n( /tmp/tmpcdpyh4woconverted.loom.test v. /tmp/tmpuybi8w1sconverted.loom.test )\nFiles /tmp/tmpcdpyh4woconverted.loom.test=41883b but /tmp/tmpuybi8w1sconverted.loom.test=28145b - compare by size (delta=10000) failed"], "status": "failure"}}, {"id": "anndata_import/0.7.5+galaxy1-6", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 6, "time_seconds": 43.780383586883545, "inputs": {"hd5_format|in|input": {"src": "hda", "id": "e3c7eeb0f0ca6e7d"}, "hd5_format|in|adata_format": "10x_h5", "hd5_format|filetype": "anndata"}, "job": {"model_class": "Job", "id": "39384e2072d8a9b2", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:01:45.824051", "update_time": "2024-09-12T19:02:04.633258", "galaxy_version": "24.1", "external_id": "gxy-vsv44", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/108/configs/tmp2pjftbwi' && python '/galaxy/server/database/jobs_directory/000/108/configs/tmp2pjftbwi'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 2, \"adata_format\": \"10x_h5\", \"input\": {\"values\": [{\"id\": 147, \"src\": \"hda\"}]}}}"}, "inputs": {"hd5_format|in|input": {"id": "e3c7eeb0f0ca6e7d", "src": "hda", "uuid": "62651f9e-98d1-4b14-af25-c810d2be8d0a"}}, "outputs": {"anndata": {"id": "d34ed2684fbd6801", "src": "hda", "uuid": "4d52c1f0-422f-4129-a9a3-8a28570252ff"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nimport scanpy as sc\nadata = sc.read_10x_h5('/galaxy/server/database/objects/6/2/6/dataset_62651f9e-98d1-4b14-af25-c810d2be8d0a.dat')\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nimport scanpy as sc\nadata = sc.read_10x_h5('/galaxy/server/database/objects/6/2/6/dataset_62651f9e-98d1-4b14-af25-c810d2be8d0a.dat')\n\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:01:51", "plugin": "core", "name": "end_epoch", "raw_value": "1726167711.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:01:47", "plugin": "core", "name": "start_epoch", "raw_value": "1726167707.0000000"}, {"title": "Memory Allocated (MB)", "value": "2152", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2152.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "anndata_import/0.7.5+galaxy1-6", "has_data": true, "data": {"tool_id": "anndata_import", "tool_version": "0.7.5+galaxy1", "test_index": 6, "time_seconds": 40.5507550239563, "inputs": {"hd5_format|in|input": {"src": "hda", "id": "f3c79a52b3653d94"}, "hd5_format|in|adata_format": "10x_h5", "hd5_format|filetype": "anndata"}, "job": {"model_class": "Job", "id": "6470afa683bc0ef9", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:06:12.831732", "update_time": "2024-09-12T19:06:30.890406", "galaxy_version": "24.1", "external_id": "gxy-2fttg", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/124/configs/tmps5fk168e' && python '/galaxy/server/database/jobs_directory/000/124/configs/tmps5fk168e'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 2, \"adata_format\": \"10x_h5\", \"input\": {\"values\": [{\"id\": 163, \"src\": \"hda\"}]}}}"}, "inputs": {"hd5_format|in|input": {"id": "f3c79a52b3653d94", "src": "hda", "uuid": "c1919c83-0bd8-42d3-907c-c1bfb0720447"}}, "outputs": {"anndata": {"id": "d4ac33fca243d9cd", "src": "hda", "uuid": "c2336e78-c749-4998-8105-7df5d957b6c9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nimport scanpy as sc\nadata = sc.read_10x_h5('/galaxy/server/database/objects/c/1/9/dataset_c1919c83-0bd8-42d3-907c-c1bfb0720447.dat')\n\nadata.write('anndata.h5ad')\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nimport scanpy as sc\nadata = sc.read_10x_h5('/galaxy/server/database/objects/c/1/9/dataset_c1919c83-0bd8-42d3-907c-c1bfb0720447.dat')\n\nadata.write('anndata.h5ad')\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:06:18", "plugin": "core", "name": "end_epoch", "raw_value": "1726167978.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:06:14", "plugin": "core", "name": "start_epoch", "raw_value": "1726167974.0000000"}, {"title": "Memory Allocated (MB)", "value": "2152", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2152.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_plugin_fixploidy/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_fixploidy", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 49.55937123298645, "inputs": {"input_file": {"src": "hda", "id": "7ee233c3297b77f3"}, "sec_plugin|ploidy_file": {"src": "hda", "id": "70bcdff51c421304"}, "sec_plugin|sex": {"src": "hda", "id": "9acee209b0156b58"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "e3507d56264a9dd3", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:23:30.208476", "update_time": "2024-09-12T19:23:50.337965", "galaxy_version": "24.1", "external_id": "gxy-c2wnc", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/0/c/dataset_f0c7bbae-b0aa-43c9-988f-188b81bf5cfc.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin fixploidy --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz -- --ploidy \"/galaxy/server/database/objects/5/d/4/dataset_5d42d35d-3cbc-411d-a739-166b6603b5d1.dat\" --sex \"/galaxy/server/database/objects/4/7/2/dataset_4724a45e-981a-417b-beb1-c90fab4d1784.dat\" --tags \"GT\" > '/galaxy/server/database/objects/0/9/8/dataset_09850473-f448-481e-8197-f9c3b5467e54.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"ploidy_file\": {\"values\": [{\"id\": 234, \"src\": \"hda\"}]}, \"sex\": {\"values\": [{\"id\": 235, \"src\": \"hda\"}]}, \"tags\": \"GT\"}", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "7ee233c3297b77f3", "src": "hda", "uuid": "f0c7bbae-b0aa-43c9-988f-188b81bf5cfc"}, "sec_plugin|ploidy_file": {"id": "70bcdff51c421304", "src": "hda", "uuid": "5d42d35d-3cbc-411d-a739-166b6603b5d1"}, "sec_plugin|sex": {"id": "9acee209b0156b58", "src": "hda", "uuid": "4724a45e-981a-417b-beb1-c90fab4d1784"}}, "outputs": {"output_file": {"id": "8f4954817c011687", "src": "hda", "uuid": "09850473-f448-481e-8197-f9c3b5467e54"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:23:36", "plugin": "core", "name": "end_epoch", "raw_value": "1726169016.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:23:35", "plugin": "core", "name": "start_epoch", "raw_value": "1726169015.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_stats/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_stats", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 79.79603695869446, "inputs": {"input_file": {"src": "hda", "id": "6fe98873a42791e5"}, "inputB_file": {"src": "hda", "id": "1d4aef326cc49aa8"}}, "job": {"model_class": "Job", "id": "663a32c8d74e11b0", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:24:15.652876", "update_time": "2024-09-12T19:25:11.053403", "galaxy_version": "24.1", "external_id": "gxy-w4f4w", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/2/5/3/dataset_253c3fc7-9b2f-4793-adcb-d3cdd7ff6f5f.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/6/c/9/dataset_6c9fa2fb-adf5-4d1e-956f-f38fde9f16ec.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools stats input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/a/1/3/dataset_a13e9d03-e3c2-44cd-b3c9-df696c24c9f1.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "plot_title": "\"\"", "sec_default": "{\"af_tag\": \"\", \"afbins\": {\"__current_case__\": 0, \"afbins_select\": \"default\"}, \"depth\": {\"__current_case__\": 0, \"set_depth\": \"no\"}, \"exons_file\": null, \"first_allele_only\": false, \"reference_source\": {\"__current_case__\": 0, \"reference_source_selector\": \"\"}, \"split_by_ID\": false, \"user_tstv\": \"\", \"verbose\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "6fe98873a42791e5", "src": "hda", "uuid": "253c3fc7-9b2f-4793-adcb-d3cdd7ff6f5f"}, "inputB_file": {"id": "1d4aef326cc49aa8", "src": "hda", "uuid": "6c9fa2fb-adf5-4d1e-956f-f38fde9f16ec"}}, "outputs": {"output_file": {"id": "4defd25e11b365d4", "src": "hda", "uuid": "a13e9d03-e3c2-44cd-b3c9-df696c24c9f1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:24:50", "plugin": "core", "name": "end_epoch", "raw_value": "1726169090.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:24:49", "plugin": "core", "name": "start_epoch", "raw_value": "1726169089.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_stats/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_stats", "tool_version": "1.15.1+galaxy4", "test_index": 1, "status": "skip"}}, {"id": "bcftools_stats/1.15.1+galaxy4-2", "has_data": true, "data": {"tool_id": "bcftools_stats", "tool_version": "1.15.1+galaxy4", "test_index": 2, "time_seconds": 64.82195806503296, "inputs": {"input_file": {"src": "hda", "id": "8dd072d5caf79b59"}, "plot_title": "Plot for mpileup.vcf"}, "job": {"model_class": "Job", "id": "731a0f6c2e09e1b3", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:25:34.707956", "update_time": "2024-09-12T19:26:15.628265", "galaxy_version": "24.1", "external_id": "gxy-sps8k", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/6/a/9/dataset_6a9bafbf-3a5a-48c1-865d-698fde536e05.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bcftools stats input0.vcf.gz > '/galaxy/server/database/objects/a/e/4/dataset_ae402fc1-724e-48b2-aa3d-f4ad6c9fa442.dat' && plot-vcfstats -p 'plot_tmp/' -T 'Plot for mpileup.vcf' -s '/galaxy/server/database/objects/a/e/4/dataset_ae402fc1-724e-48b2-aa3d-f4ad6c9fa442.dat' || (printf \"The content of plot_tmp/plot-vcfstats.log is:\\n\" >&2 && cat plot_tmp/plot-vcfstats.log >&2 && exit 1)", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "plot_title": "\"Plot for mpileup.vcf\"", "sec_default": "{\"af_tag\": \"\", \"afbins\": {\"__current_case__\": 0, \"afbins_select\": \"default\"}, \"depth\": {\"__current_case__\": 0, \"set_depth\": \"no\"}, \"exons_file\": null, \"first_allele_only\": false, \"reference_source\": {\"__current_case__\": 0, \"reference_source_selector\": \"\"}, \"split_by_ID\": false, \"user_tstv\": \"\", \"verbose\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}", "inputB_file": null}, "inputs": {"input_file": {"id": "8dd072d5caf79b59", "src": "hda", "uuid": "6a9bafbf-3a5a-48c1-865d-698fde536e05"}}, "outputs": {"output_file": {"id": "415fd2cb8c557a1f", "src": "hda", "uuid": "ae402fc1-724e-48b2-aa3d-f4ad6c9fa442"}, "output_pdf": {"id": "681ac23622859e93", "src": "hda", "uuid": "6496f0c5-c9ee-49d3-8e78-aa2c52d0b61a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Parsing bcftools stats output: /galaxy/server/database/objects/a/e/4/dataset_ae402fc1-724e-48b2-aa3d-f4ad6c9fa442.dat\nPlotting graphs: python3 plot.py\nCreating PDF: tectonic summary.tex >plot-vcfstats.log 2>&1\nFinished: plot_tmp//summary.pdf\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Parsing bcftools stats output: /galaxy/server/database/objects/a/e/4/dataset_ae402fc1-724e-48b2-aa3d-f4ad6c9fa442.dat\nPlotting graphs: python3 plot.py\nCreating PDF: tectonic summary.tex >plot-vcfstats.log 2>&1\nFinished: plot_tmp//summary.pdf\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "26 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "26.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:26:02", "plugin": "core", "name": "end_epoch", "raw_value": "1726169162.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:25:36", "plugin": "core", "name": "start_epoch", "raw_value": "1726169136.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_stats/1.15.1+galaxy4-3", "has_data": true, "data": {"tool_id": "bcftools_stats", "tool_version": "1.15.1+galaxy4", "test_index": 3, "time_seconds": 29.624394178390503, "inputs": {"input_file": {"src": "hda", "id": "1df47cc768d658ae"}, "inputB_file": {"src": "hda", "id": "36650d18141ad1f9"}, "sec_restrict|regions_overlap": "1"}, "job": {"model_class": "Job", "id": "73e4ef2f2e01965c", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4", "state": "error", "exit_code": null, "create_time": "2024-09-12T19:26:40.846878", "update_time": "2024-09-12T19:26:45.740636", "galaxy_version": "24.1", "external_id": "gxy-kkhjl", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/4/3/dataset_8435d287-38fb-4227-8d9f-8d005c03e930.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/0/e/8/dataset_0e87e6a5-9e28-4f76-9090-0931695f266f.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools stats --regions-overlap 1 input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/2/3/c/dataset_23c6ce8b-ff0e-4dce-bc53-28f0d930e12c.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "plot_title": "\"\"", "sec_default": "{\"af_tag\": \"\", \"afbins\": {\"__current_case__\": 0, \"afbins_select\": \"default\"}, \"depth\": {\"__current_case__\": 0, \"set_depth\": \"no\"}, \"exons_file\": null, \"first_allele_only\": false, \"reference_source\": {\"__current_case__\": 0, \"reference_source_selector\": \"\"}, \"split_by_ID\": false, \"user_tstv\": \"\", \"verbose\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "1df47cc768d658ae", "src": "hda", "uuid": "8435d287-38fb-4227-8d9f-8d005c03e930"}, "inputB_file": {"id": "36650d18141ad1f9", "src": "hda", "uuid": "0e87e6a5-9e28-4f76-9090-0931695f266f"}}, "outputs": {"output_file": {"id": "f40a8c5d0662968d", "src": "hda", "uuid": "23c6ce8b-ff0e-4dce-bc53-28f0d930e12c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "bcftools_stats/1.15.1+galaxy4-4", "has_data": true, "data": {"tool_id": "bcftools_stats", "tool_version": "1.15.1+galaxy4", "test_index": 4, "time_seconds": 39.01060509681702, "inputs": {"input_file": {"src": "hda", "id": "73eb2e5af2346f43"}, "sec_restrict|samples": "-"}, "job": {"model_class": "Job", "id": "2b8a0a601a5fe523", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:27:09.067487", "update_time": "2024-09-12T19:27:24.796118", "galaxy_version": "24.1", "external_id": "gxy-hkrs9", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/d/6/dataset_8d64b388-2a2b-467e-9eb3-92c04ab6f0f9.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bcftools stats --samples '-' input0.vcf.gz > '/galaxy/server/database/objects/4/8/f/dataset_48ff4a58-37da-4263-a69a-07d8a854a57a.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "plot_title": "\"\"", "sec_default": "{\"af_tag\": \"\", \"afbins\": {\"__current_case__\": 0, \"afbins_select\": \"default\"}, \"depth\": {\"__current_case__\": 0, \"set_depth\": \"no\"}, \"exons_file\": null, \"first_allele_only\": false, \"reference_source\": {\"__current_case__\": 0, \"reference_source_selector\": \"\"}, \"split_by_ID\": false, \"user_tstv\": \"\", \"verbose\": false}", "sec_restrict": "{\"apply_filters\": \"\", \"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"-\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}", "inputB_file": null}, "inputs": {"input_file": {"id": "73eb2e5af2346f43", "src": "hda", "uuid": "8d64b388-2a2b-467e-9eb3-92c04ab6f0f9"}}, "outputs": {"output_file": {"id": "13d56a543fa365f8", "src": "hda", "uuid": "48ff4a58-37da-4263-a69a-07d8a854a57a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, 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"test_index": 1, "time_seconds": 0.14823412895202637, "execution_problem": "Input staging problem: Test input file (simple_line.txt) cannot be found.", "status": "error"}}, {"id": "deeptools_plot_correlation/3.5.4+galaxy0-0", "has_data": true, "data": {"tool_id": "deeptools_plot_correlation", "tool_version": "3.5.4+galaxy0", "test_index": 0, "time_seconds": 89.73308420181274, "inputs": {"corData": {"src": "hda", "id": "7dbaf9c5b5117ca4"}, "outFileFormat": "png", "outFileCorMatrix": true}, "job": {"model_class": "Job", "id": "d5bb8b6d17283723", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T18:34:13.874521", "update_time": "2024-09-12T18:35:14.568247", "galaxy_version": "24.1", "external_id": "gxy-4rtv2", "handler": null, "job_runner_name": null, "command_line": "plotCorrelation --corData '/galaxy/server/database/objects/6/2/3/dataset_6239b2e7-88ed-4a24-baf4-0d6f810fb6ec.dat' --plotFile '/galaxy/server/database/objects/2/8/f/dataset_28f3ef1d-0543-4ecb-921d-458315a7122f.dat' --corMethod 'spearman' --whatToPlot 'heatmap' --colorMap 'RdYlBu' --plotTitle '' --plotWidth 11.0 --plotHeight 9.5 --plotFileFormat 'png' --outFileCorMatrix '/galaxy/server/database/objects/6/8/3/dataset_68343e7b-18e2-419a-8abb-45703d9b15c1.dat'", "user_email": "tests@fake.org", "command_version": "plotCorrelation 3.5.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "outFileCorMatrix": "true", "removeOutliers": "false", "outFileFormat": "\"png\"", "skipZeros": "false", "plotting_type": "{\"__current_case__\": 0, \"colorMap\": \"RdYlBu\", \"plotHeight\": \"9.5\", \"plotNumbers\": false, \"plotTitle\": \"\", \"plotWidth\": \"11.0\", \"whatToPlot\": \"heatmap\", \"zMax\": \"\", \"zMin\": \"\"}", "corMethod": 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/galaxy/server/database/objects/4/9/e/dataset_49ef5203-b32c-4310-8bfe-0ff811c42cbd.dat\n[FLASH] \n[FLASH] Output files:\n[FLASH] ./out.extendedFrags.fastq\n[FLASH] ./out.notCombined_1.fastq\n[FLASH] ./out.notCombined_2.fastq\n[FLASH] ./out.hist\n[FLASH] ./out.histogram\n[FLASH] \n[FLASH] Parameters:\n[FLASH] Min overlap: 10\n[FLASH] Max overlap: 65\n[FLASH] Max mismatch density: 0.250000\n[FLASH] Allow \"outie\" pairs: false\n[FLASH] Cap mismatch quals: false\n[FLASH] Combiner threads: 1\n[FLASH] Input format: FASTQ, phred_offset=64\n[FLASH] Output format: FASTQ, phred_offset=64\n[FLASH] \n[FLASH] Starting reader and writer threads\n[FLASH] Starting 1 combiner threads\n[FLASH] Processed 200 read pairs\n[FLASH] \n[FLASH] Read combination statistics:\n[FLASH] Total pairs: 200\n[FLASH] Combined pairs: 5\n[FLASH] Uncombined pairs: 195\n[FLASH] Percent combined: 2.50%\n[FLASH] \n[FLASH] Writing histogram files.\n[FLASH] \n[FLASH] FLASH v1.2.11 complete!\n[FLASH] 0.022 seconds elapsed\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[FLASH] Starting FLASH v1.2.11\n[FLASH] Fast Length Adjustment of SHort reads\n[FLASH] \n[FLASH] Input files:\n[FLASH] /galaxy/server/database/objects/1/a/0/dataset_1a0e5370-35b2-4f58-83df-d4ca785b0828.dat\n[FLASH] /galaxy/server/database/objects/4/9/e/dataset_49ef5203-b32c-4310-8bfe-0ff811c42cbd.dat\n[FLASH] \n[FLASH] Output files:\n[FLASH] ./out.extendedFrags.fastq\n[FLASH] ./out.notCombined_1.fastq\n[FLASH] ./out.notCombined_2.fastq\n[FLASH] ./out.hist\n[FLASH] ./out.histogram\n[FLASH] \n[FLASH] Parameters:\n[FLASH] Min overlap: 10\n[FLASH] Max overlap: 65\n[FLASH] Max mismatch density: 0.250000\n[FLASH] Allow \"outie\" pairs: false\n[FLASH] Cap mismatch quals: false\n[FLASH] Combiner threads: 1\n[FLASH] Input format: FASTQ, phred_offset=64\n[FLASH] Output format: FASTQ, phred_offset=64\n[FLASH] \n[FLASH] Starting reader and writer threads\n[FLASH] Starting 1 combiner threads\n[FLASH] Processed 200 read pairs\n[FLASH] 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--threads=${GALAXY_SLOTS:-1} -m 10 -M 65 -x 0.25 '/galaxy/server/database/objects/1/0/6/dataset_106b07b9-e5e4-4e1a-a48c-37c3c6d8b736.dat' '/galaxy/server/database/objects/f/7/1/dataset_f71cd529-91d2-4c20-95a2-fa98c86f3bd7.dat' -p 33 -z --output-suffix=''", "user_email": "tests@fake.org", "command_version": "FLASH v1.2.11", "params": {"layout": "{\"__current_case__\": 1, \"reads\": {\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}, \"select_layout\": \"collection\"}", "min_overlap": "\"10\"", "max_overlap": "\"65\"", "max_mismatch_density": "\"0.25\"", "allow_outies": "false", "generate_histogram": "false", "save_log": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"layout|reads1": {"id": "4cb3c7cd46ca3b31", "src": "hda", "uuid": "106b07b9-e5e4-4e1a-a48c-37c3c6d8b736"}, "layout|reads2": {"id": "f535697429a960af", "src": "hda", "uuid": "f71cd529-91d2-4c20-95a2-fa98c86f3bd7"}}, "outputs": {"merged_reads": {"id": "4fc50e55ceaaf610", "src": "hda", "uuid": "c93410b4-5b21-49ad-a409-5823279555eb"}, "unmerged_reads_f": {"id": "cf0a14c93d5c0da4", "src": "hda", "uuid": "6b0a6a55-b63c-4e0f-be79-2e72329afd4a"}, "unmerged_reads_r": {"id": "05264c584b20b27c", "src": "hda", "uuid": "a1321931-d7a0-4b92-90fe-242a733f12c0"}, "hist": {"id": "5911fd8579ff189d", "src": "hda", "uuid": "a700ea27-ef62-4c05-b7a5-553198774068"}, "log": {"id": "351dc77277b31b5b", "src": "hda", "uuid": "e81c8699-e7ed-41e4-a1a4-8afe1eef335f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[FLASH] Starting FLASH v1.2.11\n[FLASH] Fast Length Adjustment of SHort reads\n[FLASH] \n[FLASH] Input files:\n[FLASH] /galaxy/server/database/objects/1/0/6/dataset_106b07b9-e5e4-4e1a-a48c-37c3c6d8b736.dat\n[FLASH] /galaxy/server/database/objects/f/7/1/dataset_f71cd529-91d2-4c20-95a2-fa98c86f3bd7.dat\n[FLASH] \n[FLASH] Output files:\n[FLASH] ./out.extendedFrags.fastq\n[FLASH] ./out.notCombined_1.fastq\n[FLASH] ./out.notCombined_2.fastq\n[FLASH] ./out.hist\n[FLASH] ./out.histogram\n[FLASH] \n[FLASH] Parameters:\n[FLASH] Min overlap: 10\n[FLASH] Max overlap: 65\n[FLASH] Max mismatch density: 0.250000\n[FLASH] Allow \"outie\" pairs: false\n[FLASH] Cap mismatch quals: false\n[FLASH] Combiner threads: 1\n[FLASH] Input format: FASTQ, phred_offset=33\n[FLASH] Output format: FASTQ, phred_offset=33, gzip\n[FLASH] \n[FLASH] Starting reader and writer threads\n[FLASH] Starting 1 combiner threads\n[FLASH] Processed 500 read pairs\n[FLASH] \n[FLASH] Read combination statistics:\n[FLASH] Total pairs: 500\n[FLASH] Combined pairs: 18\n[FLASH] Uncombined pairs: 482\n[FLASH] Percent combined: 3.60%\n[FLASH] \n[FLASH] Writing histogram files.\n[FLASH] \n[FLASH] FLASH v1.2.11 complete!\n[FLASH] 0.046 seconds elapsed\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[FLASH] Starting FLASH v1.2.11\n[FLASH] Fast Length Adjustment of SHort reads\n[FLASH] \n[FLASH] Input files:\n[FLASH] /galaxy/server/database/objects/1/0/6/dataset_106b07b9-e5e4-4e1a-a48c-37c3c6d8b736.dat\n[FLASH] /galaxy/server/database/objects/f/7/1/dataset_f71cd529-91d2-4c20-95a2-fa98c86f3bd7.dat\n[FLASH] \n[FLASH] Output files:\n[FLASH] ./out.extendedFrags.fastq\n[FLASH] ./out.notCombined_1.fastq\n[FLASH] ./out.notCombined_2.fastq\n[FLASH] ./out.hist\n[FLASH] ./out.histogram\n[FLASH] \n[FLASH] Parameters:\n[FLASH] Min overlap: 10\n[FLASH] Max overlap: 65\n[FLASH] Max mismatch density: 0.250000\n[FLASH] Allow \"outie\" pairs: false\n[FLASH] Cap mismatch quals: false\n[FLASH] Combiner threads: 1\n[FLASH] Input format: FASTQ, phred_offset=33\n[FLASH] Output format: FASTQ, phred_offset=33, gzip\n[FLASH] \n[FLASH] Starting reader and writer threads\n[FLASH] Starting 1 combiner threads\n[FLASH] Processed 500 read pairs\n[FLASH] \n[FLASH] Read combination statistics:\n[FLASH] Total pairs: 500\n[FLASH] Combined pairs: 18\n[FLASH] Uncombined pairs: 482\n[FLASH] Percent combined: 3.60%\n[FLASH] \n[FLASH] Writing histogram files.\n[FLASH] \n[FLASH] FLASH v1.2.11 complete!\n[FLASH] 0.046 seconds elapsed\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 18:38:32", "plugin": "core", "name": "start_epoch", "raw_value": "1726166312.0000000"}, {"title": "Job End Time", "value": "2024-09-12 18:38:32", "plugin": "core", "name": "end_epoch", "raw_value": "1726166312.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "lofreq_call/2.1.5+galaxy2-0", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 0, "time_seconds": 38.17130255699158, "inputs": {"reads": {"src": "hda", "id": "097c9c86ae789649"}, "reference_source|ref": {"src": "hda", "id": "7299715a3323e0c8"}, "reference_source|ref_selector": "history"}, "job": {"model_class": "Job", "id": "3c9b9a9b19ed1b5d", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "state": "error", "exit_code": null, "create_time": "2024-09-12T19:20:00.208909", "update_time": "2024-09-12T19:20:14.171223", "galaxy_version": "24.1", "external_id": "gxy-96x7v", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/2/e/f/dataset_2efde3d5-4472-4a87-8ac7-b7632b2f7ae8.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/b/2/4/dataset_b24dbd0f-6326-451b-8e67-3caac826cba8.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/0/f/6/metadata_0f6bc320-32d1-42ce-8213-fe7581a6f465.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 218, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "097c9c86ae789649", "src": "hda", "uuid": "b24dbd0f-6326-451b-8e67-3caac826cba8"}, "reference_source|ref": {"id": "7299715a3323e0c8", "src": "hda", "uuid": "2efde3d5-4472-4a87-8ac7-b7632b2f7ae8"}}, "outputs": {"variants": {"id": "cebde5ad27a14bc1", "src": "hda", "uuid": "8e2a573c-380f-45b3-bd7e-39628de603c4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "INFO [2024-09-12 19:20:07,645]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 19:20:07,656]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:20:09,439]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/159/tmp/lofreq2_call_parallel3do47ktx/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "INFO [2024-09-12 19:20:07,645]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 19:20:07,656]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:20:09,439]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/159/tmp/lofreq2_call_parallel3do47ktx/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "lofreq_call/2.1.5+galaxy2-1", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 1, "time_seconds": 42.32826375961304, "inputs": {"reads": {"src": "hda", "id": "dc4934e3a2f0696f"}, "reference_source|ref": {"src": "hda", "id": "2a15824c280e0c39"}, "reference_source|ref_selector": "history", "call_control|set_call_options": "yes"}, "job": {"model_class": "Job", "id": "3aac882fa0868af6", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:20:39.096301", "update_time": "2024-09-12T19:20:56.263808", "galaxy_version": "24.1", "external_id": "gxy-cghqp", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/f/b/4/dataset_fb420fe7-f908-44f7-bbb3-fd4a113f232d.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/7/4/d/dataset_74d65b76-1497-4485-99b9-437a1d2073d8.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/c/2/b/metadata_c2b48662-d067-4ed6-a95b-a183a30979ab.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", "user_email": "tests@fake.org", "command_version": "2.1.5", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", "call_control": "{\"__current_case__\": 1, \"align_quals\": {\"alnqual\": {\"__current_case__\": 0, \"alnqual_choice\": {\"__current_case__\": 1, \"alnquals_to_use\": \"\", \"extended_baq\": true}, \"use_alnqual\": \"\"}}, \"bc_quals\": {\"alt_bq\": {\"__current_case__\": 0, \"modify\": \"\"}, \"min_alt_bq\": \"6\", \"min_bq\": \"6\"}, \"coverage\": {\"max_depth\": \"1000000\", \"min_cov\": \"1\"}, \"joint_qual\": {\"def_alt_jq\": \"0\", \"min_alt_jq\": \"0\", \"min_jq\": \"0\"}, \"map_quals\": {\"min_mq\": \"0\", \"use_mq\": {\"__current_case__\": 0, \"max_mq\": \"255\", \"no_mq\": \"\"}}, \"pe\": {\"use_orphan\": false}, \"set_call_options\": \"yes\", \"source_qual\": {\"use_src_qual\": {\"__current_case__\": 0, \"src_qual\": \"\"}}}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 221, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "dc4934e3a2f0696f", "src": "hda", "uuid": "74d65b76-1497-4485-99b9-437a1d2073d8"}, "reference_source|ref": {"id": "2a15824c280e0c39", "src": "hda", "uuid": "fb420fe7-f908-44f7-bbb3-fd4a113f232d"}}, "outputs": {"variants": {"id": "b86170180899caae", "src": "hda", "uuid": "fd00a24f-09d8-44c8-86b1-592e2e274e16"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "INFO [2024-09-12 19:20:41,176]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 19:20:41,187]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:20:42,902]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/162/tmp/lofreq2_call_parallelzqejfro5/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "INFO [2024-09-12 19:20:41,176]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 19:20:41,187]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:20:42,902]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/162/tmp/lofreq2_call_parallelzqejfro5/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:20:42", "plugin": "core", "name": "end_epoch", "raw_value": "1726168842.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:20:40", "plugin": "core", "name": "start_epoch", "raw_value": "1726168840.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "lofreq_call/2.1.5+galaxy2-2", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 2, "time_seconds": 47.85778093338013, "inputs": {"reads": {"src": "hda", "id": "9291d18f7114038e"}, "reference_source|ref": {"src": "hda", "id": "78320cb46c95d21a"}, "reference_source|ref_selector": "history", "call_control|source_qual|use_src_qual|def_nm_q": "40", "call_control|source_qual|use_src_qual|ign_vcf": {"src": "hda", "id": "0e3eb904c3811adc"}, "call_control|source_qual|use_src_qual|src_qual": "--src-qual", "call_control|set_call_options": "yes"}, "job": {"model_class": "Job", "id": "53fd8acef2b5620c", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:21:27.370034", "update_time": "2024-09-12T19:21:44.049089", "galaxy_version": "24.1", "external_id": "gxy-vzsp7", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/0/5/dataset_c05d2441-7553-44b4-b976-442762092e44.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/2/8/5/dataset_285e144e-1a3f-4de4-8208-9416f53b5e9c.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/6/1/3/metadata_6138f380-aae0-406d-b104-d00bfa6b8e93.dat' reads.bam.bai && ln -s '/galaxy/server/database/objects/f/f/5/dataset_ff50a07c-b83c-4ccd-b7a1-32ec13947a83.dat' ign0.vcf && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf 'ign0.vcf' --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", "user_email": "tests@fake.org", "command_version": "2.1.5", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", "call_control": "{\"__current_case__\": 1, \"align_quals\": {\"alnqual\": {\"__current_case__\": 0, \"alnqual_choice\": {\"__current_case__\": 1, \"alnquals_to_use\": \"\", \"extended_baq\": true}, \"use_alnqual\": \"\"}}, \"bc_quals\": {\"alt_bq\": {\"__current_case__\": 0, \"modify\": \"\"}, \"min_alt_bq\": \"6\", \"min_bq\": \"6\"}, \"coverage\": {\"max_depth\": \"1000000\", \"min_cov\": \"1\"}, \"joint_qual\": {\"def_alt_jq\": \"0\", \"min_alt_jq\": \"0\", \"min_jq\": \"0\"}, \"map_quals\": {\"min_mq\": \"0\", \"use_mq\": {\"__current_case__\": 0, \"max_mq\": \"255\", \"no_mq\": \"\"}}, \"pe\": {\"use_orphan\": false}, \"set_call_options\": \"yes\", \"source_qual\": {\"use_src_qual\": {\"__current_case__\": 1, \"def_nm_q\": \"40\", \"ign_vcf\": {\"values\": [{\"id\": 225, \"src\": \"hda\"}]}, \"src_qual\": \"--src-qual\"}}}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 224, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "9291d18f7114038e", "src": "hda", "uuid": "285e144e-1a3f-4de4-8208-9416f53b5e9c"}, "reference_source|ref": {"id": "78320cb46c95d21a", "src": "hda", "uuid": "c05d2441-7553-44b4-b976-442762092e44"}, "call_control|source_qual|use_src_qual|ign_vcf": {"id": "0e3eb904c3811adc", "src": "hda", "uuid": "ff50a07c-b83c-4ccd-b7a1-32ec13947a83"}, "call_control|source_qual|use_src_qual|ign_vcf1": {"id": "0e3eb904c3811adc", "src": "hda", "uuid": "ff50a07c-b83c-4ccd-b7a1-32ec13947a83"}}, "outputs": {"variants": {"id": "8bc3f67c291276a9", "src": "hda", "uuid": "e0e2a463-8c1b-4b06-92ac-8c6be8060c30"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "INFO [2024-09-12 19:21:28,934]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 19:21:28,945]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:21:31,012]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/166/tmp/lofreq2_call_parallelnjueji9v/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "INFO [2024-09-12 19:21:28,934]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 19:21:28,945]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:21:31,012]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/166/tmp/lofreq2_call_parallelnjueji9v/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:21:31", "plugin": "core", "name": "end_epoch", "raw_value": "1726168891.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:21:28", "plugin": "core", "name": "start_epoch", "raw_value": "1726168888.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "lofreq_call/2.1.5+galaxy2-3", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 3, "time_seconds": 42.339930295944214, "inputs": {"reads": {"src": "hda", "id": "153ea620a60827b1"}, "reference_source|ref": {"src": "hda", "id": "f87bf9da378bca57"}, "reference_source|ref_selector": "history", "filter_control|filter_type": "set_all_off"}, "job": {"model_class": "Job", "id": "5c0ae45e23f6c784", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:22:09.467027", "update_time": "2024-09-12T19:22:26.611057", "galaxy_version": "24.1", "external_id": "gxy-r6nn5", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/8/1/1/dataset_81154c7e-71fc-4459-9c29-6a18d650d952.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/9/3/d/dataset_93d2c1d0-b7bc-4a98-8d57-fbcc63f308ec.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/6/b/3/metadata_6b396935-0f2b-40be-b4cb-d6dfe1b2a5e9.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --sig 1 --bonf 1 --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && ln -s variants.vcf variants.vcf.gz && gzip -df variants.vcf.gz && echo set_all_off", "user_email": "tests@fake.org", "command_version": "2.1.5", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 0, \"bonf\": \"1\", \"filter_type\": \"set_all_off\", \"others\": \"--no-default-filter\", \"sig\": \"1\"}", "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 228, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "153ea620a60827b1", "src": "hda", "uuid": "93d2c1d0-b7bc-4a98-8d57-fbcc63f308ec"}, "reference_source|ref": {"id": "f87bf9da378bca57", "src": "hda", "uuid": "81154c7e-71fc-4459-9c29-6a18d650d952"}}, "outputs": {"variants": {"id": "5ab222eef43243f3", "src": "hda", "uuid": "3d5b86e1-ec04-425d-ba6f-ee41c9153f93"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "INFO [2024-09-12 19:22:11,755]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2024-09-12 19:22:11,766]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:22:13,482]: Copying concatenated vcf file to final destination\nset_all_off\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "INFO [2024-09-12 19:22:11,755]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2024-09-12 19:22:11,766]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:22:13,482]: Copying concatenated vcf file to final destination\nset_all_off\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:22:13", "plugin": "core", "name": "end_epoch", "raw_value": "1726168933.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:22:11", "plugin": "core", "name": "start_epoch", "raw_value": "1726168931.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "lofreq_call/2.1.5+galaxy2-4", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 4, "time_seconds": 33.04222512245178, "inputs": {"reads": {"src": "hda", "id": "b691b770366e328d"}, "reference_source|ref": {"src": "hda", "id": "e1812a2a3571e07b"}, "reference_source|ref_selector": "history", "variant_types": "--call-indels --only-indels", "filter_control|filter_type": "set_all_off"}, "job": {"model_class": "Job", "id": "aff42d3d4ee95ab5", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "state": "error", "exit_code": null, "create_time": "2024-09-12T19:22:52.190076", "update_time": "2024-09-12T19:22:59.823447", "galaxy_version": "24.1", "external_id": "gxy-cnmcz", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/3/8/c/dataset_38c16d84-ec4e-43bf-9b32-2702fb3a788d.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/3/4/1/dataset_341a5a5a-bd31-4651-8e5f-c7eb5659795a.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/1/6/0/metadata_1609f14d-df7d-467c-9de1-bc293594970f.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && ln -s variants.vcf variants.vcf.gz && gzip -df variants.vcf.gz && echo set_all_off", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 0, \"bonf\": \"1\", \"filter_type\": \"set_all_off\", \"others\": \"--no-default-filter\", \"sig\": \"1\"}", "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", "variant_types": "\"--call-indels --only-indels\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 231, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "b691b770366e328d", "src": "hda", "uuid": "341a5a5a-bd31-4651-8e5f-c7eb5659795a"}, "reference_source|ref": {"id": "e1812a2a3571e07b", "src": "hda", "uuid": "38c16d84-ec4e-43bf-9b32-2702fb3a788d"}}, "outputs": {"variants": {"id": "80316208467124cb", "src": "hda", "uuid": "1792d2f5-6231-4256-b713-625b05d9ac18"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "INFO [2024-09-12 19:22:54,460]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2024-09-12 19:22:54,472]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 0\nNumber of indel tests performed: 9\nINFO [2024-09-12 19:22:57,118]: Copying concatenated vcf file to final destination\nset_all_off\n", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "INFO [2024-09-12 19:22:54,460]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2024-09-12 19:22:54,472]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 0\nNumber of indel tests performed: 9\nINFO [2024-09-12 19:22:57,118]: Copying concatenated vcf file to final destination\nset_all_off\n", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "medaka_variant/1.7.2+galaxy1-0", "has_data": true, "data": {"tool_id": "medaka_variant", "tool_version": "1.7.2+galaxy1", "test_index": 0, "time_seconds": 86.52023935317993, "inputs": {"pool|inputs": [{"src": "hda", "id": "ee28955812120d89"}, {"src": "hda", "id": "ee28955812120d89"}], "pool|pool_mode": "Yes", "reference_source|ref_file": {"src": "hda", "id": "2c586af689b790c8"}, "reference_source|reference_source_selector": "history", "ambig_ref": true, "output_annotated|in_bam": {"src": "hda", "id": "5c9f142b579b34d2"}, "output_annotated|output_annotated_select": "true", "output_log_bool": true}, "job": {"model_class": "Job", "id": "84dfdb049c81a807", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T18:41:10.418963", "update_time": "2024-09-12T18:42:06.602834", "galaxy_version": "24.1", "external_id": "gxy-f4pf7", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/f/1/dataset_1f159152-5091-440e-b232-5288c0529a40.dat' reference.fa && medaka variant --debug --ambig_ref reference.fa '/galaxy/server/database/objects/3/8/0/dataset_380fe545-2d6c-4382-8923-c4633f1f563b.dat' '/galaxy/server/database/objects/3/8/0/dataset_380fe545-2d6c-4382-8923-c4633f1f563b.dat' raw.vcf 2>&1 | tee '/galaxy/server/database/objects/c/2/5/dataset_c25acc6a-9c8c-41c7-be5e-44381384bb46.dat' && ln -s '/galaxy/server/database/objects/e/2/f/dataset_e2faacc5-6ecc-4fa7-aebd-103cbd0bfad0.dat' in.bam && ln -s '/galaxy/server/database/objects/_metadata_files/2/c/5/metadata_2c5fece6-13d2-47fa-ab68-7604d89134ad.dat' in.bai && medaka tools annotate --dpsp --pad 25 raw.vcf reference.fa in.bam tmp.vcf && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/eb746fa6f514/medaka_variant/convert_VCF_info_fields.py' tmp.vcf '/galaxy/server/database/objects/4/8/3/dataset_4836b437-bf3e-405b-94db-bfcdee20a8f6.dat'", "user_email": "tests@fake.org", "command_version": "medaka 1.7.2", "params": {"pool": "{\"__current_case__\": 0, \"inputs\": {\"values\": [{\"id\": 48, \"src\": \"hda\"}, {\"id\": 48, \"src\": \"hda\"}]}, \"pool_mode\": \"Yes\"}", "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 49, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}", "regions": "\"\"", "verbose": "false", "ambig_ref": "true", "gvcf": "false", "output_annotated": "{\"__current_case__\": 0, \"in_bam\": {\"values\": [{\"id\": 50, \"src\": \"hda\"}]}, \"output_annotated_select\": \"true\", \"pad\": \"25\"}", "output_log_bool": "true", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"pool|inputs": {"id": "ee28955812120d89", "src": "hda", "uuid": "380fe545-2d6c-4382-8923-c4633f1f563b"}, "pool|inputs1": {"id": "ee28955812120d89", "src": "hda", "uuid": "380fe545-2d6c-4382-8923-c4633f1f563b"}, "pool|inputs2": {"id": "ee28955812120d89", "src": "hda", "uuid": "380fe545-2d6c-4382-8923-c4633f1f563b"}, "reference_source|ref_file": {"id": "2c586af689b790c8", "src": "hda", "uuid": "1f159152-5091-440e-b232-5288c0529a40"}, "output_annotated|in_bam": {"id": "5c9f142b579b34d2", "src": "hda", "uuid": "e2faacc5-6ecc-4fa7-aebd-103cbd0bfad0"}}, "outputs": {"out_variants": {"id": "7e0d5152986e8835", "src": "hda", "uuid": "4836b437-bf3e-405b-94db-bfcdee20a8f6"}, "out_log": {"id": "008775b360117abf", "src": "hda", "uuid": "c25acc6a-9c8c-41c7-be5e-44381384bb46"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[18:41:42 - DataStre] Loaded sample register.\n[18:41:42 - DataStre] Loaded sample register.\n[18:41:42 - DataIndx] Loaded 1/2 (50.00%) sample files.\n[18:41:42 - DataIndx] Loaded 2/2 (100.00%) sample files.\n[18:41:42 - Variants] Label decoding is:\n0: ('*',)\n1: ('A',)\n2: ('C',)\n3: ('G',)\n4: ('T',)\n[18:41:42 - Variants] Processing NC_045512.2:0-.\n[18:41:42 - TrimOlap] NC_045512.2:30.0-2939.0 is contained within NC_045512.2:30.0-2939.0, skipping.\n", "tool_stderr": "[18:41:45 - Annotate] Getting chrom coordinates\n[18:41:45 - Annotate] Processing chunk with coordinates: NC_045512.2:44-1813\n[18:41:45 - BAMFile] Creating pool of 16 BAM file sets.\n", "job_stdout": "", "job_stderr": "", "stdout": "[18:41:42 - DataStre] Loaded sample register.\n[18:41:42 - DataStre] Loaded sample register.\n[18:41:42 - DataIndx] Loaded 1/2 (50.00%) sample files.\n[18:41:42 - DataIndx] Loaded 2/2 (100.00%) sample files.\n[18:41:42 - Variants] Label decoding is:\n0: ('*',)\n1: ('A',)\n2: ('C',)\n3: ('G',)\n4: ('T',)\n[18:41:42 - Variants] Processing NC_045512.2:0-.\n[18:41:42 - TrimOlap] NC_045512.2:30.0-2939.0 is contained within NC_045512.2:30.0-2939.0, skipping.\n", "stderr": "[18:41:45 - Annotate] Getting chrom coordinates\n[18:41:45 - Annotate] Processing chunk with coordinates: NC_045512.2:44-1813\n[18:41:45 - BAMFile] Creating pool of 16 BAM file sets.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 18:41:38", "plugin": "core", "name": "start_epoch", "raw_value": "1726166498.0000000"}, {"title": "Job End Time", "value": "2024-09-12 18:41:46", "plugin": "core", "name": "end_epoch", "raw_value": "1726166506.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "8 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "medaka_variant/1.7.2+galaxy1-1", "has_data": true, "data": {"tool_id": "medaka_variant", "tool_version": "1.7.2+galaxy1", "test_index": 1, "time_seconds": 51.959206342697144, "inputs": {"pool|input": {"src": "hda", "id": "5c858a8da752f283"}, "pool|pool_mode": "No", "reference_source|ref_file": {"src": "hda", "id": "9b3ec3f1f110d3c4"}, "reference_source|reference_source_selector": "history", "ambig_ref": true, "output_annotated|in_bam": {"src": "hda", "id": "095ab72dfe189fb3"}, "output_annotated|output_annotated_select": "true", "output_log_bool": true}, "job": {"model_class": "Job", "id": "e5c0cb7b99d7758f", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T18:42:36.942700", "update_time": "2024-09-12T18:42:58.621570", "galaxy_version": "24.1", "external_id": "gxy-7k557", "handler": null, "job_runner_name": null, "command_line": "gunzip -c '/galaxy/server/database/objects/5/0/9/dataset_5099ee0f-4415-4d9f-9617-0132f1043c11.dat' > reference.fa && medaka variant --debug --ambig_ref reference.fa '/galaxy/server/database/objects/f/7/8/dataset_f789e6fe-a1e9-41b2-8253-03d7083371e3.dat' raw.vcf 2>&1 | tee '/galaxy/server/database/objects/d/b/e/dataset_dbe826e6-1aab-46f3-add6-55b5b0e03e56.dat' && ln -s '/galaxy/server/database/objects/8/5/f/dataset_85f7bb6f-6618-460f-b9f1-cc1c10efd360.dat' in.bam && ln -s '/galaxy/server/database/objects/_metadata_files/2/a/6/metadata_2a66d2fa-f650-4b79-9359-74a45531630a.dat' in.bai && medaka tools annotate --dpsp --pad 25 raw.vcf reference.fa in.bam tmp.vcf && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/eb746fa6f514/medaka_variant/convert_VCF_info_fields.py' tmp.vcf '/galaxy/server/database/objects/6/1/0/dataset_61088807-cedf-476a-96cf-4dfb61a9b7c8.dat'", "user_email": "tests@fake.org", "command_version": "medaka 1.7.2", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_log_bool": "true", "output_annotated": "{\"__current_case__\": 0, \"in_bam\": {\"values\": [{\"id\": 55, \"src\": \"hda\"}]}, \"output_annotated_select\": \"true\", \"pad\": \"25\"}", "gvcf": "false", "ambig_ref": "true", "verbose": "false", "regions": "\"\"", "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 54, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}", "pool": "{\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 53, \"src\": \"hda\"}]}, \"pool_mode\": \"No\"}"}, "inputs": {"pool|input": {"id": "5c858a8da752f283", "src": "hda", "uuid": "f789e6fe-a1e9-41b2-8253-03d7083371e3"}, "reference_source|ref_file": {"id": "9b3ec3f1f110d3c4", "src": "hda", "uuid": "5099ee0f-4415-4d9f-9617-0132f1043c11"}, "output_annotated|in_bam": {"id": "095ab72dfe189fb3", "src": "hda", "uuid": "85f7bb6f-6618-460f-b9f1-cc1c10efd360"}}, "outputs": {"out_variants": {"id": "d39b4356c0d01d30", "src": "hda", "uuid": "61088807-cedf-476a-96cf-4dfb61a9b7c8"}, "out_log": {"id": "d569bffeb771697d", "src": "hda", "uuid": "dbe826e6-1aab-46f3-add6-55b5b0e03e56"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[18:42:41 - DataStre] Loaded sample register.\n[18:42:41 - DataIndx] Loaded 1/1 (100.00%) sample files.\n[18:42:41 - Variants] Label decoding is:\n0: ('*',)\n1: ('A',)\n2: ('C',)\n3: ('G',)\n4: ('T',)\n[18:42:41 - Variants] Processing NC_045512.2:0-.\n", "tool_stderr": "[18:42:44 - Annotate] Getting chrom coordinates\n[18:42:44 - Annotate] Processing chunk with coordinates: NC_045512.2:44-1813\n[18:42:44 - BAMFile] Creating pool of 16 BAM file sets.\n", "job_stdout": "", "job_stderr": "", "stdout": "[18:42:41 - DataStre] Loaded sample register.\n[18:42:41 - DataIndx] Loaded 1/1 (100.00%) sample files.\n[18:42:41 - Variants] Label decoding is:\n0: ('*',)\n1: ('A',)\n2: ('C',)\n3: ('G',)\n4: ('T',)\n[18:42:41 - Variants] Processing NC_045512.2:0-.\n", "stderr": "[18:42:44 - Annotate] Getting chrom coordinates\n[18:42:44 - Annotate] Processing chunk with coordinates: NC_045512.2:44-1813\n[18:42:44 - BAMFile] Creating pool of 16 BAM file sets.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 18:42:38", "plugin": "core", "name": "start_epoch", 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"ok", "exit_code": 0, "create_time": "2024-09-12T18:43:23.032134", "update_time": "2024-09-12T18:43:41.141077", "galaxy_version": "24.1", "external_id": "gxy-82wrq", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/f/6/d/dataset_f6db7b93-949e-40da-a03d-30f731edccf0.dat' reference.fa && medaka variant --debug reference.fa '/galaxy/server/database/objects/1/6/f/dataset_16f2a446-6698-48bf-9549-5603b2a499cf.dat' '/galaxy/server/database/objects/e/0/f/dataset_e0fa5ac0-23a7-48a9-b751-2c67aa6a98f0.dat' 2>&1 | tee 'XXXX'", "user_email": "tests@fake.org", "command_version": "medaka 1.7.2", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_log_bool": "false", "output_annotated": "{\"__current_case__\": 1, \"output_annotated_select\": \"false\"}", "gvcf": "false", "ambig_ref": "false", "verbose": "false", "regions": "\"\"", "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 59, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}", "pool": "{\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 58, \"src\": \"hda\"}]}, \"pool_mode\": \"No\"}"}, "inputs": {"pool|input": {"id": "c7b1b9ca8b9b6fbc", "src": "hda", "uuid": "16f2a446-6698-48bf-9549-5603b2a499cf"}, "reference_source|ref_file": {"id": "dcc5df0733668a06", "src": "hda", "uuid": "f6db7b93-949e-40da-a03d-30f731edccf0"}}, "outputs": {"out_variants": {"id": "38c6ecde7a68c98a", "src": "hda", "uuid": "e0fa5ac0-23a7-48a9-b751-2c67aa6a98f0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[18:43:28 - DataStre] Loaded sample register.\n[18:43:28 - DataIndx] Loaded 1/1 (100.00%) sample files.\n[18:43:28 - Variants] Label decoding is:\n0: ('*',)\n1: ('A',)\n2: ('C',)\n3: ('G',)\n4: ('T',)\n[18:43:28 - Variants] Processing NC_045512.2:0-.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[18:43:28 - DataStre] Loaded sample register.\n[18:43:28 - DataIndx] Loaded 1/1 (100.00%) sample files.\n[18:43:28 - Variants] Label decoding is:\n0: ('*',)\n1: ('A',)\n2: ('C',)\n3: ('G',)\n4: ('T',)\n[18:43:28 - Variants] Processing NC_045512.2:0-.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 18:43:24", "plugin": "core", "name": "start_epoch", "raw_value": "1726166604.0000000"}, {"title": "Job End Time", "value": "2024-09-12 18:43:28", "plugin": "core", "name": "end_epoch", "raw_value": "1726166608.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}]}, "status": "success"}}, 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"plugin": "core", "name": "runtime_seconds", "raw_value": "15.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:14:15", "plugin": "core", "name": "end_epoch", "raw_value": "1726168455.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:14:00", "plugin": "core", "name": "start_epoch", "raw_value": "1726168440.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "sailfish/0.10.1.1-0", "has_data": true, "data": {"tool_id": "sailfish", "tool_version": "0.10.1.1", "test_index": 0, "time_seconds": 56.31096649169922, "inputs": {"refTranscriptSource|ownFile": {"src": "hda", "id": "9d96d267d35b97f8"}, "refTranscriptSource|TranscriptSource": "history", "single_or_paired|input_mate1": {"src": "hda", "id": "5b643a3584b3d2cc"}, "single_or_paired|input_mate2": {"src": "hda", "id": "db95d19a8092a982"}, "single_or_paired|single_or_paired_opts": "paired", "biasCorrect": false}, "job": {"model_class": "Job", "id": "5c9f142b579b34d2", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T18:47:58.071168", "update_time": "2024-09-12T18:48:24.865059", "galaxy_version": "24.1", "external_id": "gxy-krnrk", "handler": null, "job_runner_name": null, "command_line": "sailfish index --transcripts /galaxy/server/database/objects/2/6/6/dataset_266c2fc9-c20f-4354-9ee8-92c7f5f42cbf.dat --kmerSize 21 --out ./index_dir --threads \"${GALAXY_SLOTS:-4}\" && ln -s /galaxy/server/database/objects/6/a/9/dataset_6a9f9b3f-659a-4b0f-b980-af1223a30c7c.dat ./mate1.fastq && ln -s /galaxy/server/database/objects/e/a/4/dataset_ea47b2ca-47d7-41ac-b1e1-6bdecc2a4d60.dat ./mate2.fastq && sailfish quant --index ./index_dir --mates1 ./mate1.fastq --mates2 ./mate2.fastq --libType \"IU\" --output ./results --threads \"${GALAXY_SLOTS:-4}\" --gcSizeSamp 1 --gcSpeedSamp 1 --fldMean 200 --fldSD 80 --maxReadOcc 200 --maxFragLen 1000 --txpAggregationKey 'gene_id' --numBiasSamples 1000000 --numFragSamples 10000 --numGibbsSamples 0 --numBootstraps 0", "user_email": "tests@fake.org", "command_version": "version : 0.9.2", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "numBootstraps": "\"0\"", "numGibbsSamples": "\"0\"", "numFragSamples": "\"10000\"", "numBiasSamples": "\"1000000\"", "allowDovetail": "false", "enforceLibCompat": "false", "ignoreLibCompat": "false", "txpAggregationKey": "\"gene_id\"", "maxFragLen": "\"1000\"", "unsmoothedFLD": "false", "discardOrphans": "false", "useVBOpt": "false", "noEffectiveLengthCorrection": "false", "maxReadOcc": "\"200\"", "fldSD": "\"80\"", "fldMean": "\"200\"", "strictIntersect": "false", "gcSpeedSamp": "\"1\"", "gcSizeSamp": "\"1\"", "dumpEq": "false", "gcBiasCorrect": "false", "biasCorrect": "false", "geneMap": null, "single_or_paired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 72, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 73, \"src\": \"hda\"}]}, \"orientation\": \"I\", \"single_or_paired_opts\": \"paired\", \"strandedness\": \"U\"}", "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"kmerSize\": \"21\", \"ownFile\": {\"values\": [{\"id\": 71, \"src\": \"hda\"}]}}"}, "inputs": {"single_or_paired|input_mate1": {"id": "5b643a3584b3d2cc", "src": "hda", "uuid": "6a9f9b3f-659a-4b0f-b980-af1223a30c7c"}, "single_or_paired|input_mate2": {"id": "db95d19a8092a982", "src": "hda", "uuid": "ea47b2ca-47d7-41ac-b1e1-6bdecc2a4d60"}, "refTranscriptSource|ownFile": {"id": "9d96d267d35b97f8", "src": "hda", "uuid": "266c2fc9-c20f-4354-9ee8-92c7f5f42cbf"}}, "outputs": {"output_quant": {"id": "de61d63a05be4330", "src": "hda", "uuid": "bc6a6efa-9641-484c-8e91-242954394c52"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.0016581s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 6.5245e-05s\nWriting sequence data to file . . . done\nElapsed time: 8.2072e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000134942s\ndone\nElapsed time: 0.00345343s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00153581s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { ./mate1.fastq }\n# [ mates2 ] => { ./mate2.fastq }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:48:10.091] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:48:10.182] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:48:10.186] [jointLog] [info] done\n[2024-09-12 18:48:10.184] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:48:10.184] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:48:10.185] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:48:10.186] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:48:10.186] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:48:10.186] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:48:10.186] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:48:10.186] [stderrLog] [info] Done loading index\n\n[2024-09-12 18:48:10.209] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:48:10.209] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:48:10.210] [jointLog] [info] Estimating effective lengths\nDone Quasi-Mapping \n\n[2024-09-12 18:48:10.220] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:48:10.220] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:48:10.220] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:48:10.221] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:48:10.221] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:48:10.221] [jointLog] [info] iteration = 64 | max rel diff. = 0.00117687\n[2024-09-12 18:48:10.221] [jointLog] [info] Finished optimizer\n[2024-09-12 18:48:10.221] [jointLog] [info] writing output \n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.0016581s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 6.5245e-05s\nWriting sequence data to file . . . done\nElapsed time: 8.2072e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000134942s\ndone\nElapsed time: 0.00345343s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00153581s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { ./mate1.fastq }\n# [ mates2 ] => { ./mate2.fastq }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:48:10.091] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:48:10.182] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:48:10.186] [jointLog] [info] done\n[2024-09-12 18:48:10.184] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:48:10.184] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:48:10.185] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:48:10.186] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:48:10.186] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:48:10.186] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:48:10.186] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:48:10.186] [stderrLog] [info] Done loading index\n\n[2024-09-12 18:48:10.209] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:48:10.209] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:48:10.210] [jointLog] [info] Estimating effective lengths\nDone Quasi-Mapping \n\n[2024-09-12 18:48:10.220] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:48:10.220] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:48:10.220] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:48:10.221] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:48:10.221] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:48:10.221] [jointLog] [info] iteration = 64 | max rel diff. = 0.00117687\n[2024-09-12 18:48:10.221] [jointLog] [info] Finished optimizer\n[2024-09-12 18:48:10.221] [jointLog] [info] writing output \n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 18:48:10", "plugin": "core", "name": "end_epoch", "raw_value": "1726166890.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 18:48:08", "plugin": "core", "name": "start_epoch", "raw_value": "1726166888.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "sailfish/0.10.1.1-1", "has_data": true, "data": {"tool_id": "sailfish", "tool_version": "0.10.1.1", "test_index": 1, "time_seconds": 34.74197864532471, "inputs": {"refTranscriptSource|ownFile": {"src": "hda", "id": "168c5019d723e181"}, "refTranscriptSource|TranscriptSource": "history", "single_or_paired|input_mate1": {"src": "hda", "id": "d35b1c9b91227c0a"}, "single_or_paired|input_mate2": {"src": "hda", "id": "6f2c1b5a12d2a732"}, "single_or_paired|single_or_paired_opts": "paired", "biasCorrect": false}, "job": {"model_class": "Job", "id": "9b3ec3f1f110d3c4", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1", "state": "error", "exit_code": null, "create_time": "2024-09-12T18:48:54.088211", "update_time": "2024-09-12T18:48:59.647494", "galaxy_version": "24.1", "external_id": "gxy-hdlsq", "handler": null, "job_runner_name": null, "command_line": "sailfish index --transcripts /galaxy/server/database/objects/3/4/9/dataset_3494bf84-f97b-49e7-98a5-8789e9f8d5bc.dat --kmerSize 21 --out ./index_dir --threads \"${GALAXY_SLOTS:-4}\" && ln -s /galaxy/server/database/objects/6/1/6/dataset_616dd9f5-0f3b-42b2-9491-7b78b6283fee.dat ./mate1.fastq && ln -s /galaxy/server/database/objects/9/f/f/dataset_9ff10746-bcea-4d0e-b556-3bd5e22b6e1c.dat ./mate2.fastq && sailfish quant --index ./index_dir --mates1 <(zcat ./mate1.fastq) --mates2 <(zcat ./mate2.fastq) --libType \"IU\" --output ./results --threads \"${GALAXY_SLOTS:-4}\" --gcSizeSamp 1 --gcSpeedSamp 1 --fldMean 200 --fldSD 80 --maxReadOcc 200 --maxFragLen 1000 --txpAggregationKey 'gene_id' --numBiasSamples 1000000 --numFragSamples 10000 --numGibbsSamples 0 --numBootstraps 0", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "numBootstraps": "\"0\"", "numGibbsSamples": "\"0\"", "numFragSamples": "\"10000\"", "numBiasSamples": "\"1000000\"", "allowDovetail": "false", "enforceLibCompat": "false", "ignoreLibCompat": "false", "txpAggregationKey": "\"gene_id\"", "maxFragLen": "\"1000\"", "unsmoothedFLD": "false", "discardOrphans": "false", "useVBOpt": "false", "noEffectiveLengthCorrection": "false", "maxReadOcc": "\"200\"", "fldSD": "\"80\"", "fldMean": "\"200\"", "strictIntersect": "false", "gcSpeedSamp": "\"1\"", "gcSizeSamp": "\"1\"", "dumpEq": "false", "gcBiasCorrect": "false", "biasCorrect": "false", "geneMap": null, "single_or_paired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 76, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 77, \"src\": \"hda\"}]}, \"orientation\": \"I\", \"single_or_paired_opts\": \"paired\", \"strandedness\": \"U\"}", "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"kmerSize\": \"21\", \"ownFile\": {\"values\": [{\"id\": 75, \"src\": \"hda\"}]}}"}, "inputs": {"single_or_paired|input_mate2": {"id": "6f2c1b5a12d2a732", "src": "hda", "uuid": "9ff10746-bcea-4d0e-b556-3bd5e22b6e1c"}, "refTranscriptSource|ownFile": {"id": "168c5019d723e181", "src": "hda", "uuid": "3494bf84-f97b-49e7-98a5-8789e9f8d5bc"}, "single_or_paired|input_mate1": {"id": "d35b1c9b91227c0a", "src": "hda", "uuid": "616dd9f5-0f3b-42b2-9491-7b78b6283fee"}}, "outputs": {"output_quant": {"id": "4c335ad89d24fbaa", "src": "hda", "uuid": "0cf1dc2f-2051-4722-9ea2-00d8c9e388a0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.00110978s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 3.7451e-05s\nWriting sequence data to file . . . done\nElapsed time: 6.5654e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000113315s\ndone\nElapsed time: 0.00327229s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00145451s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { /dev/fd/63 }\n# [ mates2 ] => { /dev/fd/62 }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:48:56.748] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:48:56.842] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:48:56.843] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:48:56.843] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:48:56.843] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:48:56.843] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:48:56.843] [stderrLog] [info] Done loading index\n\n[2024-09-12 18:48:56.839] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:48:56.843] [jointLog] [info] done\n[2024-09-12 18:48:56.864] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:48:56.864] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:48:56.865] [jointLog] [info] Estimating effective lengths\nDone Quasi-Mapping \n\n[2024-09-12 18:48:56.875] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:48:56.875] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:48:56.875] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:48:56.876] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 64 | max rel diff. = 0.00117687\n[2024-09-12 18:48:56.876] [jointLog] [info] Finished optimizer\n[2024-09-12 18:48:56.876] [jointLog] [info] writing output \n\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.00110978s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 3.7451e-05s\nWriting sequence data to file . . . done\nElapsed time: 6.5654e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000113315s\ndone\nElapsed time: 0.00327229s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00145451s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { /dev/fd/63 }\n# [ mates2 ] => { /dev/fd/62 }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:48:56.748] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:48:56.842] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:48:56.843] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:48:56.843] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:48:56.843] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:48:56.843] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:48:56.843] [stderrLog] [info] Done loading index\n\n[2024-09-12 18:48:56.839] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:48:56.843] [jointLog] [info] done\n[2024-09-12 18:48:56.864] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:48:56.864] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:48:56.865] [jointLog] [info] Estimating effective lengths\nDone Quasi-Mapping \n\n[2024-09-12 18:48:56.875] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:48:56.875] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:48:56.875] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:48:56.876] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 64 | max rel diff. = 0.00117687\n[2024-09-12 18:48:56.876] [jointLog] [info] Finished optimizer\n[2024-09-12 18:48:56.876] [jointLog] [info] writing output \n\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, exit_code: None, stderr: Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.00110978s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 3.7451e-05s\nWriting sequence data to file . . . done\nElapsed time: 6.5654e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000113315s\ndone\nElapsed time: 0.00327229s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00145451s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { /dev/fd/63 }\n# [ mates2 ] => { /dev/fd/62 }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:48:56.748] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:48:56.842] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:48:56.843] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:48:56.843] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:48:56.843] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:48:56.843] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:48:56.843] [stderrLog] [info] Done loading index\n\n[2024-09-12 18:48:56.839] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:48:56.843] [jointLog] [info] done\n[2024-09-12 18:48:56.864] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:48:56.864] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:48:56.865] [jointLog] [info] Estimating effective lengths\nDone Quasi-Mapping \n\n[2024-09-12 18:48:56.875] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:48:56.875] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:48:56.875] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:48:56.876] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 64 | max rel diff. = 0.00117687\n[2024-09-12 18:48:56.876] [jointLog] [info] Finished optimizer\n[2024-09-12 18:48:56.876] [jointLog] [info] writing output \n\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, exit_code: None, stderr: Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.00110978s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 3.7451e-05s\nWriting sequence data to file . . . done\nElapsed time: 6.5654e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000113315s\ndone\nElapsed time: 0.00327229s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00145451s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { /dev/fd/63 }\n# [ mates2 ] => { /dev/fd/62 }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:48:56.748] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:48:56.842] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:48:56.843] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:48:56.843] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:48:56.843] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:48:56.843] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:48:56.843] [stderrLog] [info] Done loading index\n\n[2024-09-12 18:48:56.839] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:48:56.843] [jointLog] [info] done\n[2024-09-12 18:48:56.864] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:48:56.864] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:48:56.865] [jointLog] [info] Estimating effective lengths\nDone Quasi-Mapping \n\n[2024-09-12 18:48:56.875] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:48:56.875] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:48:56.875] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:48:56.876] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 64 | max rel diff. = 0.00117687\n[2024-09-12 18:48:56.876] [jointLog] [info] Finished optimizer\n[2024-09-12 18:48:56.876] [jointLog] [info] writing output \n\n."], "status": "failure"}}, {"id": "sailfish/0.10.1.1-2", "has_data": true, "data": {"tool_id": "sailfish", "tool_version": "0.10.1.1", "test_index": 2, "time_seconds": 47.10543394088745, "inputs": {"refTranscriptSource|ownFile": {"src": "hda", "id": "07295b63630cd388"}, "refTranscriptSource|TranscriptSource": "history", "single_or_paired|input_mate1": {"src": "hda", "id": "859213c2a6222ab9"}, "single_or_paired|input_mate2": {"src": "hda", "id": "f491a846e11318f6"}, "single_or_paired|single_or_paired_opts": "paired", "biasCorrect": true}, "job": {"model_class": "Job", "id": "c7b1b9ca8b9b6fbc", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T18:49:29.548907", "update_time": "2024-09-12T18:49:46.736156", "galaxy_version": "24.1", "external_id": "gxy-lrp6j", "handler": null, "job_runner_name": null, "command_line": "sailfish index --transcripts /galaxy/server/database/objects/a/a/7/dataset_aa72f395-628d-415b-acce-2803e6114b15.dat --kmerSize 21 --out ./index_dir --threads \"${GALAXY_SLOTS:-4}\" && ln -s /galaxy/server/database/objects/1/8/8/dataset_18868b01-5f77-4e5a-ace9-65ed0394cf96.dat ./mate1.fastq && ln -s /galaxy/server/database/objects/e/6/e/dataset_e6e4c4b8-8229-4406-ba8b-8b3b7a53bd09.dat ./mate2.fastq && sailfish quant --index ./index_dir --mates1 ./mate1.fastq --mates2 ./mate2.fastq --libType \"IU\" --output ./results --biasCorrect --threads \"${GALAXY_SLOTS:-4}\" --gcSizeSamp 1 --gcSpeedSamp 1 --fldMean 200 --fldSD 80 --maxReadOcc 200 --maxFragLen 1000 --txpAggregationKey 'gene_id' --numBiasSamples 1000000 --numFragSamples 10000 --numGibbsSamples 0 --numBootstraps 0", "user_email": "tests@fake.org", "command_version": "version : 0.9.2", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "numBootstraps": "\"0\"", "numGibbsSamples": "\"0\"", "numFragSamples": "\"10000\"", "numBiasSamples": "\"1000000\"", "allowDovetail": "false", "enforceLibCompat": "false", "ignoreLibCompat": "false", "txpAggregationKey": "\"gene_id\"", "maxFragLen": "\"1000\"", "unsmoothedFLD": "false", "discardOrphans": "false", "useVBOpt": "false", "noEffectiveLengthCorrection": "false", "maxReadOcc": "\"200\"", "fldSD": "\"80\"", "fldMean": "\"200\"", "strictIntersect": "false", "gcSpeedSamp": "\"1\"", "gcSizeSamp": "\"1\"", "dumpEq": "false", "gcBiasCorrect": "false", "biasCorrect": "true", "geneMap": null, "single_or_paired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 80, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 81, \"src\": \"hda\"}]}, \"orientation\": \"I\", \"single_or_paired_opts\": \"paired\", \"strandedness\": \"U\"}", "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"kmerSize\": \"21\", \"ownFile\": {\"values\": [{\"id\": 79, \"src\": \"hda\"}]}}"}, "inputs": {"refTranscriptSource|ownFile": {"id": "07295b63630cd388", "src": "hda", "uuid": "aa72f395-628d-415b-acce-2803e6114b15"}, "single_or_paired|input_mate1": {"id": "859213c2a6222ab9", "src": "hda", "uuid": "18868b01-5f77-4e5a-ace9-65ed0394cf96"}, "single_or_paired|input_mate2": {"id": "f491a846e11318f6", "src": "hda", "uuid": "e6e4c4b8-8229-4406-ba8b-8b3b7a53bd09"}}, "outputs": {"output_quant": {"id": "2e470f49e54464da", "src": "hda", "uuid": "5785f478-b66b-48f7-ba96-0ba7e6e42648"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.00116881s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 4.3419e-05s\nWriting sequence data to file . . . done\nElapsed time: 6.7568e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000117723s\ndone\nElapsed time: 0.0119619s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00152346s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { ./mate1.fastq }\n# [ mates2 ] => { ./mate2.fastq }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ biasCorrect ] => { }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:49:33.097] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:49:33.187] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:49:33.191] [jointLog] [info] done\n\n[2024-09-12 18:49:33.214] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:49:33.214] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:49:33.215] [jointLog] [info] Estimating effective lengths\n[2024-09-12 18:49:33.188] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:49:33.188] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:49:33.189] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:49:33.190] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:49:33.190] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:49:33.190] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:49:33.190] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:49:33.191] [stderrLog] [info] Done loading index\nDone Quasi-Mapping \n\n[2024-09-12 18:49:33.225] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:49:33.225] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:49:33.226] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:49:33.226] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:49:33.226] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:49:33.226] [jointLog] [info] iteration 50, recomputing effective lengths\n[2024-09-12 18:49:33.228] [jointLog] [info] iteration = 63 | max rel diff. = 0.00199953\n[2024-09-12 18:49:33.228] [jointLog] [info] Finished optimizer\n[2024-09-12 18:49:33.228] [jointLog] [info] writing output \n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.00116881s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 4.3419e-05s\nWriting sequence data to file . . . done\nElapsed time: 6.7568e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000117723s\ndone\nElapsed time: 0.0119619s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00152346s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { ./mate1.fastq }\n# [ mates2 ] => { ./mate2.fastq }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ biasCorrect ] => { }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:49:33.097] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:49:33.187] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:49:33.191] [jointLog] [info] done\n\n[2024-09-12 18:49:33.214] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:49:33.214] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:49:33.215] [jointLog] [info] Estimating effective lengths\n[2024-09-12 18:49:33.188] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:49:33.188] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:49:33.189] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:49:33.190] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:49:33.190] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:49:33.190] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:49:33.190] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:49:33.191] [stderrLog] [info] Done loading index\nDone Quasi-Mapping \n\n[2024-09-12 18:49:33.225] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:49:33.225] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:49:33.226] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:49:33.226] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:49:33.226] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:49:33.226] [jointLog] [info] iteration 50, recomputing effective lengths\n[2024-09-12 18:49:33.228] [jointLog] [info] iteration = 63 | max rel diff. = 0.00199953\n[2024-09-12 18:49:33.228] [jointLog] [info] Finished optimizer\n[2024-09-12 18:49:33.228] [jointLog] [info] writing output \n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 18:49:33", "plugin": "core", "name": "end_epoch", "raw_value": "1726166973.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 18:49:31", "plugin": "core", "name": "start_epoch", "raw_value": "1726166971.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "sailfish/0.10.1.1-3", "has_data": true, "data": {"tool_id": "sailfish", "tool_version": "0.10.1.1", "test_index": 3, "time_seconds": 52.70718026161194, "inputs": {"refTranscriptSource|ownFile": {"src": "hda", "id": "2e3546eb0c2a0f11"}, "refTranscriptSource|TranscriptSource": "history", "single_or_paired|input_mate1": {"src": "hda", "id": "92087b09cfc8a7f1"}, "single_or_paired|input_mate2": {"src": "hda", "id": "129531a63b7a5513"}, "single_or_paired|single_or_paired_opts": "paired", "geneMap": {"src": "hda", "id": "43691146cb9acd87"}, "biasCorrect": true}, "job": {"model_class": "Job", "id": "3932b8f998703360", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T18:50:21.823128", "update_time": "2024-09-12T18:50:39.012948", "galaxy_version": "24.1", "external_id": "gxy-9h6pj", "handler": null, "job_runner_name": null, "command_line": "sailfish index --transcripts /galaxy/server/database/objects/e/c/4/dataset_ec45d89a-6fba-44db-ad89-2c29ce4f0335.dat --kmerSize 21 --out ./index_dir --threads \"${GALAXY_SLOTS:-4}\" && ln -s /galaxy/server/database/objects/6/5/4/dataset_654c2d19-417c-482e-8c8a-3ce38ca90c2a.dat ./mate1.fastq && ln -s /galaxy/server/database/objects/4/e/b/dataset_4eb37b3d-a366-40b4-aacf-b047b9b6132b.dat ./mate2.fastq && ln -s \"/galaxy/server/database/objects/5/7/b/dataset_57b4e349-20b4-4a25-892a-cc85166cadcf.dat\" ./geneMap.tabular && sailfish quant --index ./index_dir --mates1 ./mate1.fastq --mates2 ./mate2.fastq --libType \"IU\" --output ./results --biasCorrect --threads \"${GALAXY_SLOTS:-4}\" --gcSizeSamp 1 --gcSpeedSamp 1 --fldMean 200 --fldSD 80 --maxReadOcc 200 --geneMap ./geneMap.tabular --maxFragLen 1000 --txpAggregationKey 'gene_id' --numBiasSamples 1000000 --numFragSamples 10000 --numGibbsSamples 0 --numBootstraps 0", "user_email": "tests@fake.org", "command_version": "version : 0.9.2", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "numBootstraps": "\"0\"", "numGibbsSamples": "\"0\"", "numFragSamples": "\"10000\"", "numBiasSamples": "\"1000000\"", "allowDovetail": "false", "enforceLibCompat": "false", "ignoreLibCompat": "false", "txpAggregationKey": "\"gene_id\"", "maxFragLen": "\"1000\"", "unsmoothedFLD": "false", "discardOrphans": "false", "useVBOpt": "false", "noEffectiveLengthCorrection": "false", "maxReadOcc": "\"200\"", "fldSD": "\"80\"", "fldMean": "\"200\"", "strictIntersect": "false", "gcSpeedSamp": "\"1\"", "gcSizeSamp": "\"1\"", "dumpEq": "false", "gcBiasCorrect": "false", "biasCorrect": "true", "single_or_paired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 84, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 85, \"src\": \"hda\"}]}, \"orientation\": \"I\", \"single_or_paired_opts\": \"paired\", \"strandedness\": \"U\"}", "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"kmerSize\": \"21\", \"ownFile\": {\"values\": [{\"id\": 83, \"src\": \"hda\"}]}}"}, "inputs": {"refTranscriptSource|ownFile": {"id": "2e3546eb0c2a0f11", "src": "hda", "uuid": "ec45d89a-6fba-44db-ad89-2c29ce4f0335"}, "single_or_paired|input_mate1": {"id": "92087b09cfc8a7f1", "src": "hda", "uuid": "654c2d19-417c-482e-8c8a-3ce38ca90c2a"}, "single_or_paired|input_mate2": {"id": "129531a63b7a5513", "src": "hda", "uuid": "4eb37b3d-a366-40b4-aacf-b047b9b6132b"}, "geneMap": {"id": "43691146cb9acd87", "src": "hda", "uuid": "57b4e349-20b4-4a25-892a-cc85166cadcf"}}, "outputs": {"output_quant": {"id": "48068ee1e0edd97f", "src": "hda", "uuid": "acf22ea7-c4d8-496e-be02-61718aab2d45"}, "output_gene_quant": {"id": "d5891e03661115e3", "src": "hda", "uuid": "8a466efa-e022-46c8-aa88-1805632b7141"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.00103705s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 4.5269e-05s\nWriting sequence data to file . . . done\nElapsed time: 7.0662e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000117512s\ndone\nElapsed time: 0.00337464s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00152505s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { ./mate1.fastq }\n# [ mates2 ] => { ./mate2.fastq }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ biasCorrect ] => { }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ geneMap ] => { ./geneMap.tabular }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:50:25.571] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:50:25.666] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:50:25.666] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:50:25.667] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:50:25.667] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:50:25.667] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:50:25.668] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:50:25.668] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:50:25.668] [stderrLog] [info] Done loading index\n[2024-09-12 18:50:25.664] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:50:25.668] [jointLog] [info] done\n\n[2024-09-12 18:50:25.695] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:50:25.695] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:50:25.696] [jointLog] [info] Estimating effective lengths\nDone Quasi-Mapping \n\n[2024-09-12 18:50:25.707] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:50:25.707] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:50:25.707] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:50:25.708] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:50:25.708] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:50:25.708] [jointLog] [info] iteration 50, recomputing effective lengths\n[2024-09-12 18:50:25.710] [jointLog] [info] iteration = 63 | max rel diff. = 0.00199953\n[2024-09-12 18:50:25.710] [jointLog] [info] Finished optimizer\n[2024-09-12 18:50:25.710] [jointLog] [info] writing output \n\nComputing gene-level abundance estimates\nThere were 3 transcripts mapping to 3 genes\nWARNING: couldn't find transcript named [NR_031764]; returning transcript as it's own gene\n\ndone\nAggregating expressions to gene level . . . done\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Version Info: This is the most recent version of Sailfish\nwriting log to ./index_dir/logs/sailfish_index.log\nRapMap Indexer\n\n[Step 1 of 4] : counting k-mers\nElapsed time: 0.00103705s\n\nReplaced 0 non-ATCG nucleotides\nClipped poly-A tails from 0 transcripts\nBuilding rank-select dictionary and saving to disk done\nElapsed time: 4.5269e-05s\nWriting sequence data to file . . . done\nElapsed time: 7.0662e-05s\n[info] Building 32-bit suffix array (length of generalized text is 28577)\nBuilding suffix array . . . success\nsaving to disk . . . done\nElapsed time: 0.000117512s\ndone\nElapsed time: 0.00337464s\n\r\rprocessed 0 positions\nkhash had 18955 keys\nsaving hash to disk . . . done\nElapsed time: 0.00152505s\nVersion Info: This is the most recent version of Sailfish\n# sailfish (quasi-mapping-based) v0.9.2\n# [ program ] => sailfish \n# [ command ] => quant \n# [ index ] => { ./index_dir }\n# [ mates1 ] => { ./mate1.fastq }\n# [ mates2 ] => { ./mate2.fastq }\n# [ libType ] => { IU }\n# [ output ] => { ./results }\n# [ biasCorrect ] => { }\n# [ threads ] => { 6 }\n# [ gcSizeSamp ] => { 1 }\n# [ gcSpeedSamp ] => { 1 }\n# [ fldMean ] => { 200 }\n# [ fldSD ] => { 80 }\n# [ maxReadOcc ] => { 200 }\n# [ geneMap ] => { ./geneMap.tabular }\n# [ maxFragLen ] => { 1000 }\n# [ txpAggregationKey ] => { gene_id }\n# [ numBiasSamples ] => { 1000000 }\n# [ numFragSamples ] => { 10000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\nLogs will be written to ./results/logs\n[2024-09-12 18:50:25.571] [jointLog] [info] parsing read library format\nthere is 1 lib\nLoading 32-bit quasi indexIndex contained 15 targets\nLoaded targets\n\n\n[2024-09-12 18:50:25.666] [stderrLog] [info] Loading Suffix Array \n[2024-09-12 18:50:25.666] [stderrLog] [info] Loading Position Hash\n[2024-09-12 18:50:25.667] [stderrLog] [info] Loading Transcript Info \n[2024-09-12 18:50:25.667] [stderrLog] [info] Loading Rank-Select Bit Array\n[2024-09-12 18:50:25.667] [stderrLog] [info] There were 15 set bits in the bit array\n[2024-09-12 18:50:25.668] [stderrLog] [info] Computing transcript lengths\n[2024-09-12 18:50:25.668] [stderrLog] [info] Waiting to finish loading hash\n[2024-09-12 18:50:25.668] [stderrLog] [info] Done loading index\n[2024-09-12 18:50:25.664] [jointLog] [info] Loading Quasi index\n[2024-09-12 18:50:25.668] [jointLog] [info] done\n\n[2024-09-12 18:50:25.695] [jointLog] [info] Gathered fragment lengths from all threads\n[2024-09-12 18:50:25.695] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction\n[2024-09-12 18:50:25.696] [jointLog] [info] Estimating effective lengths\nDone Quasi-Mapping \n\n[2024-09-12 18:50:25.707] [jointLog] [info] Computed 21 rich equivalence classes for further processing\n[2024-09-12 18:50:25.707] [jointLog] [info] Counted 10000 total reads in the equivalence classes \n[2024-09-12 18:50:25.707] [jointLog] [info] Starting optimizer:\n\n[2024-09-12 18:50:25.708] [jointLog] [info] Optimizing over 21 equivalence classes\n[2024-09-12 18:50:25.708] [jointLog] [info] iteration = 0 | max rel diff. = 14.873\n[2024-09-12 18:50:25.708] [jointLog] [info] iteration 50, recomputing effective lengths\n[2024-09-12 18:50:25.710] [jointLog] [info] iteration = 63 | max rel diff. = 0.00199953\n[2024-09-12 18:50:25.710] [jointLog] [info] Finished optimizer\n[2024-09-12 18:50:25.710] [jointLog] [info] writing output \n\nComputing gene-level abundance estimates\nThere were 3 transcripts mapping to 3 genes\nWARNING: couldn't find transcript named [NR_031764]; returning transcript as it's own gene\n\ndone\nAggregating expressions to gene level . . . done\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-12 18:50:26", "plugin": "core", "name": "end_epoch", "raw_value": "1726167026.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 18:50:24", "plugin": "core", "name": "start_epoch", "raw_value": "1726167024.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "samtools_mpileup/2.1.7-0", "has_data": true, "data": {"tool_id": "samtools_mpileup", "tool_version": "2.1.7", "test_index": 0, "time_seconds": 12.585728168487549, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "samtools_mpileup/2.1.7-1", "has_data": true, "data": {"tool_id": "samtools_mpileup", "tool_version": "2.1.7", "test_index": 1, "time_seconds": 42.890095710754395, "inputs": {"input": {"src": "hda", "id": "0a36ad0bce1b08d3"}, "addref_cond|ref": {"src": "hda", "id": "f54ecdbe2e8a2f91"}, "addref_cond|addref_select": "history", "advanced_options|filter_by_flags|exclude_flags": ["4", "16"], "advanced_options|filter_by_flags|filter_flags": "filter", "advanced_options|limit_by_region|region_paste": "17:1050-1060", "advanced_options|limit_by_region|limit_by_regions": "limit", "advanced_options|disable_probabilistic_realignment": true, "advanced_options|advanced_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "f491a846e11318f6", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.7", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T18:54:59.109124", "update_time": "2024-09-12T18:55:17.345839", "galaxy_version": "24.1", "external_id": "gxy-w5jhl", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/0/6/a/dataset_06a52a64-cd57-4e74-a587-4201250111c0.dat' '0' && ln -s '/galaxy/server/database/objects/_metadata_files/8/0/0/metadata_800fe437-7a17-40f6-a2b8-9ef3e1d0ef03.dat' '0.bai' && reffa=\"reference.fa\" && ln -s '/galaxy/server/database/objects/5/3/b/dataset_53b81aef-408e-4b8b-9a8a-47546fd3c8df.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools mpileup -f \"$reffa\" '0' --rf 0 --ff 20 -r '17:1050-1060' -B -C 0 -d 8000 -q 0 -Q 13 --output '/galaxy/server/database/objects/4/2/3/dataset_4235af4f-6e3e-450b-a6bc-288f17e66c2f.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.16)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options_cond": "{\"__current_case__\": 0, \"output_options_selector\": \"default\"}", "advanced_options": "{\"__current_case__\": 1, \"advanced_options_selector\": \"advanced\", \"coefficient_for_downgrading\": \"0\", \"disable_probabilistic_realignment\": true, \"exclude_read_group\": {\"__current_case__\": 2, \"exclude_read_groups\": \"no_limit\"}, \"extended_BAQ_computation\": false, \"filter_by_flags\": {\"__current_case__\": 0, \"exclude_flags\": [\"4\", \"16\"], \"filter_flags\": \"filter\", \"require_flags\": null}, \"ignore_overlaps\": false, \"limit_by_region\": {\"__current_case__\": 0, \"bed_regions\": null, \"limit_by_regions\": \"limit\", \"region_paste\": \"17:1050-1060\"}, \"max_reads_per_bam\": \"8000\", \"minimum_base_quality\": \"13\", \"minimum_mapping_quality\": \"0\", \"qualities_illumina_onethree\": false, \"skip_anomalous_read_pairs\": false}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 120, \"src\": \"hda\"}]}}"}, "inputs": {"input": {"id": 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"job": {"model_class": "Job", "id": "60f6839817a5fb2a", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:14:54.728793", "update_time": "2024-09-12T19:15:51.005469", "galaxy_version": "24.1", "external_id": "gxy-k2t9q", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/c/4/f/dataset_c4fb42f9-4dba-46c7-9f2a-d966e9a9c1f1.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/146/configs/tmpb0geyd4v' > '/galaxy/server/database/objects/5/3/0/dataset_53090415-0c3c-4661-8c8c-98930e7c063f.dat' && python '/galaxy/server/database/jobs_directory/000/146/configs/tmpb0geyd4v' >> '/galaxy/server/database/objects/5/3/0/dataset_53090415-0c3c-4661-8c8c-98930e7c063f.dat' && ls . >> '/galaxy/server/database/objects/5/3/0/dataset_53090415-0c3c-4661-8c8c-98930e7c063f.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"exclude_highly_expressed\": {\"__current_case__\": 1, \"exclude_highly_expressed\": \"False\"}, \"key_added\": \"n_counts\", \"layer_norm\": \"None\", \"layers\": \"all\", \"method\": \"pp.normalize_total\", \"target_sum\": \"\"}"}, "inputs": {"adata": {"id": "4bfd870073202856", "src": "hda", "uuid": "c4fb42f9-4dba-46c7-9f2a-d966e9a9c1f1"}}, "outputs": {"anndata_out": {"id": "750f9dfa5e7d0fb1", "src": "hda", "uuid": "186dc834-c484-4394-9458-d42bb9af59d8"}, "hidden_output": {"id": "08c7839dc2def796", "src": "hda", "uuid": "53090415-0c3c-4661-8c8c-98930e7c063f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- n_counts\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- n_counts\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:15:28", "plugin": "core", "name": "end_epoch", "raw_value": "1726168528.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:15:23", "plugin": "core", "name": "start_epoch", "raw_value": "1726168523.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_normalize/1.9.6+galaxy4-1", "has_data": true, "data": {"tool_id": "scanpy_normalize", "tool_version": "1.9.6+galaxy4", "test_index": 1, "time_seconds": 44.08603072166443, "inputs": {"adata": {"src": "hda", "id": "c525c5c8eed7044f"}, "method|n_top_genes": "1000", "method|log": true, "method|method": "pp.recipe_zheng17", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "d34ed2684fbd6801", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:16:14.338259", "update_time": "2024-09-12T19:16:34.572526", "galaxy_version": "24.1", "external_id": "gxy-wtpfd", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/8/7/c/dataset_87caffea-6ea9-4132-aed6-d57d0898feaa.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/148/configs/tmpex32d4ns' > '/galaxy/server/database/objects/b/0/7/dataset_b07cea06-e1c6-4967-a535-b7eebe11c992.dat' && python '/galaxy/server/database/jobs_directory/000/148/configs/tmpex32d4ns' >> '/galaxy/server/database/objects/b/0/7/dataset_b07cea06-e1c6-4967-a535-b7eebe11c992.dat' && ls . >> '/galaxy/server/database/objects/b/0/7/dataset_b07cea06-e1c6-4967-a535-b7eebe11c992.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 1, \"log\": true, \"method\": \"pp.recipe_zheng17\", \"n_top_genes\": \"1000\"}"}, "inputs": {"adata": {"id": "c525c5c8eed7044f", "src": "hda", "uuid": "87caffea-6ea9-4132-aed6-d57d0898feaa"}}, "outputs": {"anndata_out": {"id": "2464284391e87a2d", "src": "hda", "uuid": "409554a7-a586-4acf-8a72-f27567e8d9c0"}, "hidden_output": {"id": "4aa5dd7697fb6f5f", "src": "hda", "uuid": "b07cea06-e1c6-4967-a535-b7eebe11c992"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 998\n[obs]\n- n_counts_all\n[var]\n- n_counts\n- mean\n- std\n[uns]\n- log1p\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 998\n[obs]\n- n_counts_all\n[var]\n- n_counts\n- mean\n- std\n[uns]\n- log1p\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:16:21", "plugin": "core", "name": "end_epoch", "raw_value": "1726168581.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:16:16", "plugin": "core", "name": "start_epoch", "raw_value": "1726168576.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_normalize/1.9.6+galaxy4-2", "has_data": true, "data": {"tool_id": "scanpy_normalize", "tool_version": "1.9.6+galaxy4", "test_index": 2, "time_seconds": 44.92133975028992, "inputs": {"adata": {"src": "hda", "id": "46d8fb730c051688"}, "method|log": true, "method|mean_threshold": "0.01", "method|cv_threshold": "2.0", "method|n_pcs": "50", "method|svd_solver": "randomized", "method|random_state": "0", "method|method": "pp.recipe_weinreb17", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "7164e81b0d7425b0", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:16:58.829750", "update_time": "2024-09-12T19:17:20.248229", "galaxy_version": "24.1", "external_id": "gxy-w7hp2", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/4/2/9/dataset_4291b546-a322-4648-be96-a6cf7d6d6f00.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/150/configs/tmpt0z908cx' > '/galaxy/server/database/objects/2/5/f/dataset_25f28bf3-53f7-4703-b0f9-864b589189b6.dat' && python '/galaxy/server/database/jobs_directory/000/150/configs/tmpt0z908cx' >> '/galaxy/server/database/objects/2/5/f/dataset_25f28bf3-53f7-4703-b0f9-864b589189b6.dat' && ls . >> '/galaxy/server/database/objects/2/5/f/dataset_25f28bf3-53f7-4703-b0f9-864b589189b6.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 2, \"cv_threshold\": \"2.0\", \"log\": true, \"mean_threshold\": \"0.01\", \"method\": \"pp.recipe_weinreb17\", \"n_pcs\": \"50\", \"random_state\": \"0\", \"svd_solver\": \"randomized\"}"}, "inputs": {"adata": {"id": "46d8fb730c051688", "src": "hda", "uuid": "4291b546-a322-4648-be96-a6cf7d6d6f00"}}, "outputs": {"anndata_out": {"id": "2acc6249fcfccc2b", "src": "hda", "uuid": "df58f810-be09-4607-a818-7d124fe7d363"}, "hidden_output": {"id": "fa1aac05ec4d2466", "src": "hda", "uuid": "25f28bf3-53f7-4703-b0f9-864b589189b6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 100 \u00d7 1592\n[obs]\n- paul15_clusters\n[uns]\n- iroot\n- log1p\n[obsm]\n- X_pca\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 100 \u00d7 1592\n[obs]\n- paul15_clusters\n[uns]\n- iroot\n- log1p\n[obsm]\n- X_pca\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:17:06", "plugin": "core", "name": "end_epoch", "raw_value": "1726168626.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:17:00", "plugin": "core", "name": "start_epoch", "raw_value": "1726168620.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_normalize/1.9.6+galaxy4-3", "has_data": true, "data": {"tool_id": "scanpy_normalize", "tool_version": "1.9.6+galaxy4", "test_index": 3, "time_seconds": 43.01812386512756, "inputs": {"adata": {"src": "hda", "id": "76ed879be1c2136c"}, "method|log": true, "method|method": "pp.recipe_seurat", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "016055815d296980", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:17:43.444529", "update_time": "2024-09-12T19:18:03.226221", "galaxy_version": "24.1", "external_id": "gxy-7rnl5", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/8/4/a/dataset_84a24ece-fb2f-43f0-9c88-a7c553fdc262.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/152/configs/tmp_i4q_h9t' > '/galaxy/server/database/objects/5/5/8/dataset_558d6663-0a03-4ace-82e2-4dad4a527c9b.dat' && python '/galaxy/server/database/jobs_directory/000/152/configs/tmp_i4q_h9t' >> '/galaxy/server/database/objects/5/5/8/dataset_558d6663-0a03-4ace-82e2-4dad4a527c9b.dat' && ls . >> '/galaxy/server/database/objects/5/5/8/dataset_558d6663-0a03-4ace-82e2-4dad4a527c9b.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 3, \"log\": true, \"method\": \"pp.recipe_seurat\"}"}, "inputs": {"adata": {"id": "76ed879be1c2136c", "src": "hda", "uuid": "84a24ece-fb2f-43f0-9c88-a7c553fdc262"}}, "outputs": {"anndata_out": {"id": "ef15555c664d22f3", "src": "hda", "uuid": "7338ec15-1fd9-45c6-86a2-027c5c2992f3"}, "hidden_output": {"id": "07e274d6f20c4350", "src": "hda", "uuid": "558d6663-0a03-4ace-82e2-4dad4a527c9b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 1\n[obs]\n- n_counts_all\n- n_genes\n[var]\n- n_counts\n- mean\n- std\n- n_cells\n[uns]\n- log1p\n", "tool_stderr": "WARNING: adata.X seems to be already log-transformed.\n", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 1\n[obs]\n- n_counts_all\n- n_genes\n[var]\n- n_counts\n- mean\n- std\n- n_cells\n[uns]\n- log1p\n", "stderr": "WARNING: adata.X seems to be already log-transformed.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:17:50", "plugin": "core", "name": "end_epoch", "raw_value": "1726168670.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:17:45", "plugin": "core", "name": "start_epoch", "raw_value": "1726168665.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_normalize/1.9.6+galaxy4-4", "has_data": true, "data": {"tool_id": "scanpy_normalize", "tool_version": "1.9.6+galaxy4", "test_index": 4, "time_seconds": 43.27221179008484, "inputs": {"adata": {"src": "hda", "id": "705ea1fc975d238d"}, "method|name_list": "all_genes", "method|t": "-1", "method|n_pca": "5", "method|method": "external.pp.magic", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "6a36c29e1ea63497", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:18:26.733499", "update_time": "2024-09-12T19:18:46.544956", "galaxy_version": "24.1", "external_id": "gxy-njdhb", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/e/9/f/dataset_e9f67249-24be-4960-a0ac-a11c3e1f4913.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/154/configs/tmpudx8uhw7' > '/galaxy/server/database/objects/7/c/f/dataset_7cfb4d6d-66a5-46cb-8d0f-c1ccbf1cd9bd.dat' && python '/galaxy/server/database/jobs_directory/000/154/configs/tmpudx8uhw7' >> '/galaxy/server/database/objects/7/c/f/dataset_7cfb4d6d-66a5-46cb-8d0f-c1ccbf1cd9bd.dat' && ls . >> '/galaxy/server/database/objects/7/c/f/dataset_7cfb4d6d-66a5-46cb-8d0f-c1ccbf1cd9bd.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 4, \"decay\": \"1\", \"knn\": \"5\", \"knn_dist\": \"euclidean\", \"knn_max\": \"\", \"method\": \"external.pp.magic\", \"n_pca\": \"5\", \"name_list\": \"all_genes\", \"random_state\": \"0\", \"solver\": \"exact\", \"t\": \"-1\"}"}, "inputs": {"adata": {"id": "705ea1fc975d238d", "src": "hda", "uuid": "e9f67249-24be-4960-a0ac-a11c3e1f4913"}}, "outputs": {"anndata_out": {"id": "3a071f39cdba8f39", "src": "hda", "uuid": "6d361eef-2a80-4858-9ad9-9c851a70963e"}, "hidden_output": {"id": "881dbc0ee8b2d077", "src": "hda", "uuid": "7cfb4d6d-66a5-46cb-8d0f-c1ccbf1cd9bd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2024-09-12 19:18:34", "plugin": "core", "name": "end_epoch", "raw_value": "1726168714.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 19:18:28", "plugin": "core", "name": "start_epoch", "raw_value": "1726168708.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_normalize/1.9.6+galaxy4-5", "has_data": true, "data": {"tool_id": "scanpy_normalize", "tool_version": "1.9.6+galaxy4", "test_index": 5, "time_seconds": 44.296324253082275, "inputs": {"adata": {"src": "hda", "id": "c1c962e7486897e1"}, "method|name_list": "pca_only", "method|t": "3", "method|n_pca": "5", "method|method": "external.pp.magic", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "1e7eb26eab8a29b7", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T19:19:10.403331", "update_time": "2024-09-12T19:19:30.910228", "galaxy_version": "24.1", "external_id": "gxy-dpgsl", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/f/7/dataset_0f7c50a1-c767-473b-9e61-4a4e53958af4.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/156/configs/tmpl9byzcnx' > '/galaxy/server/database/objects/f/a/6/dataset_fa625a1a-c4d4-4b53-93b1-9597201fe9ec.dat' && python '/galaxy/server/database/jobs_directory/000/156/configs/tmpl9byzcnx' >> '/galaxy/server/database/objects/f/a/6/dataset_fa625a1a-c4d4-4b53-93b1-9597201fe9ec.dat' && ls . >> '/galaxy/server/database/objects/f/a/6/dataset_fa625a1a-c4d4-4b53-93b1-9597201fe9ec.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 4, \"decay\": \"1\", \"knn\": \"5\", \"knn_dist\": \"euclidean\", \"knn_max\": \"\", \"method\": \"external.pp.magic\", \"n_pca\": \"5\", \"name_list\": \"pca_only\", \"random_state\": \"0\", \"solver\": \"exact\", \"t\": \"3\"}"}, "inputs": {"adata": {"id": "c1c962e7486897e1", "src": "hda", "uuid": "0f7c50a1-c767-473b-9e61-4a4e53958af4"}}, "outputs": {"anndata_out": {"id": "0b016bbeccb98d8a", "src": "hda", "uuid": "2a4b52bf-0cac-4cf2-8add-2d8c8f6dd113"}, "hidden_output": {"id": "7f7b55af4955dafb", "src": "hda", "uuid": "fa625a1a-c4d4-4b53-93b1-9597201fe9ec"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n[obsm]\n- X_magic\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 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tidyselect_1.1.1 munsell_0.5.0 \n [5] colorspace_2.0-1 R6_2.5.0 rlang_0.4.11 fansi_0.5.0 \n [9] grid_4.0.5 gtable_0.3.0 utf8_1.2.1 withr_2.4.2 \n[13] ellipsis_0.3.2 digest_0.6.27 tibble_3.1.2 lifecycle_1.0.0 \n[17] crayon_1.4.1 purrr_0.3.4 farver_2.1.0 vctrs_0.3.8 \n[21] glue_1.4.2 labeling_0.4.2 compiler_4.0.5 pillar_1.6.1 \n[25] generics_0.1.0 scales_1.1.1 pkgconfig_2.0.3 \n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, exit_code: None, stderr: Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6, exit_code: None, stderr: Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n."], "status": "failure"}}, {"id": "volcanoplot/0.0.6-1", "has_data": true, "data": {"tool_id": "volcanoplot", "tool_version": "0.0.6", "test_index": 1, "time_seconds": 45.014113426208496, "inputs": {"input": {"src": "hda", "id": "b921f920f2f0c5c5"}, "fdr_col": "4", "pval_col": "3", "lfc_col": "2", "label_col": "1", "lfc_thresh": "0", "labels|label_file": {"src": "hda", "id": "cbbc4ddf6fc5a56d"}, "labels|label_select": "file"}, "job": {"model_class": "Job", "id": "accec78088c642c0", "history_id": "7dbaf9c5b5117ca4", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6", "state": "ok", "exit_code": 0, "create_time": "2024-09-12T18:40:04.222293", "update_time": "2024-09-12T18:40:25.533390", "galaxy_version": "24.1", "external_id": "gxy-js9sd", "handler": null, "job_runner_name": null, "command_line": "Rscript '/galaxy/server/database/jobs_directory/000/23/configs/tmp4z36_u1o'", "user_email": "tests@fake.org", "command_version": "R version 4.0.5 (2021-03-31) -- \"Shake and Throw\", ggplot2 version 3.3.3, ggrepel version 0.9.1, dplyr version 1.0.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "out_options": "{\"rscript_out\": false}", "plot_options": "{\"boxes\": false, \"legend\": null, \"legend_labs\": \"Down,Not Sig,Up\", \"title\": null, \"xlab\": null, \"xmax\": \"\", \"xmin\": \"\", \"ylab\": null, \"ymax\": \"\"}", "labels": "{\"__current_case__\": 1, \"label_file\": {\"values\": [{\"id\": 44, \"src\": \"hda\"}]}, \"label_select\": \"file\"}", "lfc_thresh": "\"0.0\"", "signif_thresh": "\"0.05\"", "label_col": "\"1\"", "lfc_col": "\"2\"", "pval_col": "\"3\"", "fdr_col": "\"4\"", "header": "\"auto\""}, "inputs": {"labels|label_file": {"id": "cbbc4ddf6fc5a56d", "src": "hda", "uuid": "ab6bc997-3cbd-41b2-a7c6-50aadc113326"}, "input": {"id": "b921f920f2f0c5c5", "src": "hda", "uuid": "b6dfcf55-de0b-40bb-8d32-3d63c4bf8811"}}, "outputs": {"plot": {"id": "8544f36ebf32bf8b", "src": "hda", "uuid": "51356825-6686-4452-bed7-df37f1c1cddb"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[1] \"Header row detected\"\nnull device \n 1 \nR version 4.0.5 (2021-03-31)\nPlatform: x86_64-conda-linux-gnu (64-bit)\nRunning under: Debian GNU/Linux 10 (buster)\n\nMatrix products: default\nBLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.15.so\n\nlocale:\n [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 \n [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 \n [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C \n[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C \n\nattached base packages:\n[1] stats graphics grDevices utils datasets methods base \n\nother attached packages:\n[1] ggrepel_0.9.1 ggplot2_3.3.3 dplyr_1.0.6 \n\nloaded via a namespace (and not attached):\n [1] Rcpp_1.0.6 magrittr_2.0.1 tidyselect_1.1.1 munsell_0.5.0 \n [5] colorspace_2.0-1 R6_2.5.0 rlang_0.4.11 fansi_0.5.0 \n [9] grid_4.0.5 gtable_0.3.0 utf8_1.2.1 withr_2.4.2 \n[13] ellipsis_0.3.2 digest_0.6.27 tibble_3.1.2 lifecycle_1.0.0 \n[17] crayon_1.4.1 purrr_0.3.4 farver_2.1.0 vctrs_0.3.8 \n[21] glue_1.4.2 labeling_0.4.2 compiler_4.0.5 pillar_1.6.1 \n[25] generics_0.1.0 scales_1.1.1 pkgconfig_2.0.3 \n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"Header row detected\"\nnull device \n 1 \nR version 4.0.5 (2021-03-31)\nPlatform: x86_64-conda-linux-gnu (64-bit)\nRunning under: Debian GNU/Linux 10 (buster)\n\nMatrix products: default\nBLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.15.so\n\nlocale:\n [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 \n [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 \n [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C \n[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C \n\nattached base packages:\n[1] stats graphics grDevices utils datasets methods base \n\nother attached packages:\n[1] ggrepel_0.9.1 ggplot2_3.3.3 dplyr_1.0.6 \n\nloaded via a namespace (and not attached):\n [1] Rcpp_1.0.6 magrittr_2.0.1 tidyselect_1.1.1 munsell_0.5.0 \n [5] colorspace_2.0-1 R6_2.5.0 rlang_0.4.11 fansi_0.5.0 \n [9] grid_4.0.5 gtable_0.3.0 utf8_1.2.1 withr_2.4.2 \n[13] ellipsis_0.3.2 digest_0.6.27 tibble_3.1.2 lifecycle_1.0.0 \n[17] crayon_1.4.1 purrr_0.3.4 farver_2.1.0 vctrs_0.3.8 \n[21] glue_1.4.2 labeling_0.4.2 compiler_4.0.5 pillar_1.6.1 \n[25] generics_0.1.0 scales_1.1.1 pkgconfig_2.0.3 \n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-09-12 18:40:06", "plugin": "core", "name": "start_epoch", "raw_value": "1726166406.0000000"}, {"title": "Job End Time", "value": "2024-09-12 18:40:12", "plugin": "core", "name": "end_epoch", "raw_value": "1726166412.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "volcanoplot/0.0.6-2", "has_data": true, "data": {"tool_id": "volcanoplot", "tool_version": "0.0.6", "test_index": 2, "time_seconds": 13.910500526428223, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}], "galaxy_url": "http://34.138.42.75:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.xunit b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.xunit new file mode 100644 index 000000000..ea33616d3 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/results.xunit @@ -0,0 +1,1020 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + plot-vcfstats.log 2>&1Finished: plot_tmp//summary.pdf + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sailfish # [ command ] => quant # [ index ] => { ./index_dir }# [ mates1 ] => { ./mate1.fastq }# [ mates2 ] => { ./mate2.fastq }# [ libType ] => { IU }# [ output ] => { ./results }# [ threads ] => { 6 }# [ gcSizeSamp ] => { 1 }# [ gcSpeedSamp ] => { 1 }# [ fldMean ] => { 200 }# [ fldSD ] => { 80 }# [ maxReadOcc ] => { 200 }# [ maxFragLen ] => { 1000 }# [ txpAggregationKey ] => { gene_id }# [ numBiasSamples ] => { 1000000 }# [ numFragSamples ] => { 10000 }# [ numGibbsSamples ] => { 0 }# [ numBootstraps ] => { 0 }Logs will be written to ./results/logs[2024-09-12 18:48:10.091] [jointLog] [info] parsing read library formatthere is 1 libLoading 32-bit quasi indexIndex contained 15 targetsLoaded targets[2024-09-12 18:48:10.182] [jointLog] [info] Loading Quasi index[2024-09-12 18:48:10.186] [jointLog] [info] done[2024-09-12 18:48:10.184] [stderrLog] [info] Loading Suffix Array [2024-09-12 18:48:10.184] [stderrLog] [info] Loading Position Hash[2024-09-12 18:48:10.185] [stderrLog] [info] Loading Transcript Info [2024-09-12 18:48:10.186] [stderrLog] [info] Loading Rank-Select Bit Array[2024-09-12 18:48:10.186] [stderrLog] [info] There were 15 set bits in the bit array[2024-09-12 18:48:10.186] [stderrLog] [info] Computing transcript lengths[2024-09-12 18:48:10.186] [stderrLog] [info] Waiting to finish loading hash[2024-09-12 18:48:10.186] [stderrLog] [info] Done loading index[2024-09-12 18:48:10.209] [jointLog] [info] Gathered fragment lengths from all threads[2024-09-12 18:48:10.209] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction[2024-09-12 18:48:10.210] [jointLog] [info] Estimating effective lengthsDone Quasi-Mapping [2024-09-12 18:48:10.220] [jointLog] [info] Computed 21 rich equivalence classes for further processing[2024-09-12 18:48:10.220] [jointLog] [info] Counted 10000 total reads in the equivalence classes [2024-09-12 18:48:10.220] [jointLog] [info] Starting optimizer:[2024-09-12 18:48:10.221] [jointLog] [info] Optimizing over 21 equivalence classes[2024-09-12 18:48:10.221] [jointLog] [info] iteration = 0 | max rel diff. = 14.873[2024-09-12 18:48:10.221] [jointLog] [info] iteration = 64 | max rel diff. = 0.00117687[2024-09-12 18:48:10.221] [jointLog] [info] Finished optimizer[2024-09-12 18:48:10.221] [jointLog] [info] writing output + ]]> + + + + + + + + + + sailfish # [ command ] => quant # [ index ] => { ./index_dir }# [ mates1 ] => { /dev/fd/63 }# [ mates2 ] => { /dev/fd/62 }# [ libType ] => { IU }# [ output ] => { ./results }# [ threads ] => { 6 }# [ gcSizeSamp ] => { 1 }# [ gcSpeedSamp ] => { 1 }# [ fldMean ] => { 200 }# [ fldSD ] => { 80 }# [ maxReadOcc ] => { 200 }# [ maxFragLen ] => { 1000 }# [ txpAggregationKey ] => { gene_id }# [ numBiasSamples ] => { 1000000 }# [ numFragSamples ] => { 10000 }# [ numGibbsSamples ] => { 0 }# [ numBootstraps ] => { 0 }Logs will be written to ./results/logs[2024-09-12 18:48:56.748] [jointLog] [info] parsing read library formatthere is 1 libLoading 32-bit quasi indexIndex contained 15 targetsLoaded targets[2024-09-12 18:48:56.841] [stderrLog] [info] Loading Suffix Array [2024-09-12 18:48:56.841] [stderrLog] [info] Loading Position Hash[2024-09-12 18:48:56.842] [stderrLog] [info] Loading Transcript Info [2024-09-12 18:48:56.843] [stderrLog] [info] Loading Rank-Select Bit Array[2024-09-12 18:48:56.843] [stderrLog] [info] There were 15 set bits in the bit array[2024-09-12 18:48:56.843] [stderrLog] [info] Computing transcript lengths[2024-09-12 18:48:56.843] [stderrLog] [info] Waiting to finish loading hash[2024-09-12 18:48:56.843] [stderrLog] [info] Done loading index[2024-09-12 18:48:56.839] [jointLog] [info] Loading Quasi index[2024-09-12 18:48:56.843] [jointLog] [info] done[2024-09-12 18:48:56.864] [jointLog] [info] Gathered fragment lengths from all threads[2024-09-12 18:48:56.864] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction[2024-09-12 18:48:56.865] [jointLog] [info] Estimating effective lengthsDone Quasi-Mapping [2024-09-12 18:48:56.875] [jointLog] [info] Computed 21 rich equivalence classes for further processing[2024-09-12 18:48:56.875] [jointLog] [info] Counted 10000 total reads in the equivalence classes [2024-09-12 18:48:56.875] [jointLog] [info] Starting optimizer:[2024-09-12 18:48:56.876] [jointLog] [info] Optimizing over 21 equivalence classes[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 0 | max rel diff. = 14.873[2024-09-12 18:48:56.876] [jointLog] [info] iteration = 64 | max rel diff. = 0.00117687[2024-09-12 18:48:56.876] [jointLog] [info] Finished optimizer[2024-09-12 18:48:56.876] [jointLog] [info] writing output + ]]> + + + + + + + + sailfish # [ command ] => quant # [ index ] => { ./index_dir }# [ mates1 ] => { ./mate1.fastq }# [ mates2 ] => { ./mate2.fastq }# [ libType ] => { IU }# [ output ] => { ./results }# [ biasCorrect ] => { }# [ threads ] => { 6 }# [ gcSizeSamp ] => { 1 }# [ gcSpeedSamp ] => { 1 }# [ fldMean ] => { 200 }# [ fldSD ] => { 80 }# [ maxReadOcc ] => { 200 }# [ maxFragLen ] => { 1000 }# [ txpAggregationKey ] => { gene_id }# [ numBiasSamples ] => { 1000000 }# [ numFragSamples ] => { 10000 }# [ numGibbsSamples ] => { 0 }# [ numBootstraps ] => { 0 }Logs will be written to ./results/logs[2024-09-12 18:49:33.097] [jointLog] [info] parsing read library formatthere is 1 libLoading 32-bit quasi indexIndex contained 15 targetsLoaded targets[2024-09-12 18:49:33.187] [jointLog] [info] Loading Quasi index[2024-09-12 18:49:33.191] [jointLog] [info] done[2024-09-12 18:49:33.214] [jointLog] [info] Gathered fragment lengths from all threads[2024-09-12 18:49:33.214] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction[2024-09-12 18:49:33.215] [jointLog] [info] Estimating effective lengths[2024-09-12 18:49:33.188] [stderrLog] [info] Loading Suffix Array [2024-09-12 18:49:33.188] [stderrLog] [info] Loading Position Hash[2024-09-12 18:49:33.189] [stderrLog] [info] Loading Transcript Info [2024-09-12 18:49:33.190] [stderrLog] [info] Loading Rank-Select Bit Array[2024-09-12 18:49:33.190] [stderrLog] [info] There were 15 set bits in the bit array[2024-09-12 18:49:33.190] [stderrLog] [info] Computing transcript lengths[2024-09-12 18:49:33.190] [stderrLog] [info] Waiting to finish loading hash[2024-09-12 18:49:33.191] [stderrLog] [info] Done loading indexDone Quasi-Mapping [2024-09-12 18:49:33.225] [jointLog] [info] Computed 21 rich equivalence classes for further processing[2024-09-12 18:49:33.225] [jointLog] [info] Counted 10000 total reads in the equivalence classes [2024-09-12 18:49:33.226] [jointLog] [info] Starting optimizer:[2024-09-12 18:49:33.226] [jointLog] [info] Optimizing over 21 equivalence classes[2024-09-12 18:49:33.226] [jointLog] [info] iteration = 0 | max rel diff. = 14.873[2024-09-12 18:49:33.226] [jointLog] [info] iteration 50, recomputing effective lengths[2024-09-12 18:49:33.228] [jointLog] [info] iteration = 63 | max rel diff. = 0.00199953[2024-09-12 18:49:33.228] [jointLog] [info] Finished optimizer[2024-09-12 18:49:33.228] [jointLog] [info] writing output + ]]> + + + + + + + + sailfish # [ command ] => quant # [ index ] => { ./index_dir }# [ mates1 ] => { ./mate1.fastq }# [ mates2 ] => { ./mate2.fastq }# [ libType ] => { IU }# [ output ] => { ./results }# [ biasCorrect ] => { }# [ threads ] => { 6 }# [ gcSizeSamp ] => { 1 }# [ gcSpeedSamp ] => { 1 }# [ fldMean ] => { 200 }# [ fldSD ] => { 80 }# [ maxReadOcc ] => { 200 }# [ geneMap ] => { ./geneMap.tabular }# [ maxFragLen ] => { 1000 }# [ txpAggregationKey ] => { gene_id }# [ numBiasSamples ] => { 1000000 }# [ numFragSamples ] => { 10000 }# [ numGibbsSamples ] => { 0 }# [ numBootstraps ] => { 0 }Logs will be written to ./results/logs[2024-09-12 18:50:25.571] [jointLog] [info] parsing read library formatthere is 1 libLoading 32-bit quasi indexIndex contained 15 targetsLoaded targets[2024-09-12 18:50:25.666] [stderrLog] [info] Loading Suffix Array [2024-09-12 18:50:25.666] [stderrLog] [info] Loading Position Hash[2024-09-12 18:50:25.667] [stderrLog] [info] Loading Transcript Info [2024-09-12 18:50:25.667] [stderrLog] [info] Loading Rank-Select Bit Array[2024-09-12 18:50:25.667] [stderrLog] [info] There were 15 set bits in the bit array[2024-09-12 18:50:25.668] [stderrLog] [info] Computing transcript lengths[2024-09-12 18:50:25.668] [stderrLog] [info] Waiting to finish loading hash[2024-09-12 18:50:25.668] [stderrLog] [info] Done loading index[2024-09-12 18:50:25.664] [jointLog] [info] Loading Quasi index[2024-09-12 18:50:25.668] [jointLog] [info] done[2024-09-12 18:50:25.695] [jointLog] [info] Gathered fragment lengths from all threads[2024-09-12 18:50:25.695] [jointLog] [warning] Sailfish saw fewer then 10000 uniquely mapped reads so 200 will be used as the mean fragment length and 80 as the standard deviation for effective length correction[2024-09-12 18:50:25.696] [jointLog] [info] Estimating effective lengthsDone Quasi-Mapping [2024-09-12 18:50:25.707] [jointLog] [info] Computed 21 rich equivalence classes for further processing[2024-09-12 18:50:25.707] [jointLog] [info] Counted 10000 total reads in the equivalence classes [2024-09-12 18:50:25.707] [jointLog] [info] Starting optimizer:[2024-09-12 18:50:25.708] [jointLog] [info] Optimizing over 21 equivalence classes[2024-09-12 18:50:25.708] [jointLog] [info] iteration = 0 | max rel diff. = 14.873[2024-09-12 18:50:25.708] [jointLog] [info] iteration 50, recomputing effective lengths[2024-09-12 18:50:25.710] [jointLog] [info] iteration = 63 | max rel diff. = 0.00199953[2024-09-12 18:50:25.710] [jointLog] [info] Finished optimizer[2024-09-12 18:50:25.710] [jointLog] [info] writing output Computing gene-level abundance estimatesThere were 3 transcripts mapping to 3 genesWARNING: couldn't find transcript named [NR_031764]; returning transcript as it's own genedoneAggregating expressions to gene level . . . done + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/tools.yml b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/tools.yml new file mode 100644 index 000000000..3e6e35213 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/tools.yml @@ -0,0 +1,126 @@ +chunk: 7 +tools: +- name: collection_element_identifiers + owner: iuc + revisions: + - d3c07d270a50 + tool_panel_section_id: collection_operations + tool_panel_section_label: Collection Operations +- name: deeptools_plot_correlation + owner: bgruening + revisions: + - 32e451def88c + tool_panel_section_id: deeptools + tool_panel_section_label: deepTools +- name: flash + owner: iuc + revisions: + - a27654fc4270 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: volcanoplot + owner: iuc + revisions: + - 73b8cb5bddcd + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: medaka_variant + owner: iuc + revisions: + - 43815fa60f3a + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: poretools_times + owner: iuc + revisions: + - 960be5e0b47e + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: sailfish + owner: bgruening + revisions: + - a8f343909c17 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: samtools_phase + owner: devteam + revisions: + - b5c3b1856370 + - 1e5880498f52 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_mpileup + owner: devteam + revisions: + - fa7ad9b89f4a + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: anndata_import + owner: iuc + revisions: + - 55e35e9203cf + - fb9e030ffae4 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: raceid_inspecttrajectory + owner: iuc + revisions: + - c8434a623268 + - df8e4e54d367 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_normalize + owner: iuc + revisions: + - ab55fe8030b6 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_scale_data + owner: ebi-gxa + revisions: + - 9664a6c00fd1 + - c6e52529260e + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: regex_find_replace + owner: galaxyp + revisions: + - ae8c4b2488e7 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: lofreq_call + owner: iuc + revisions: + - e1461b5c52a0 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: bcftools_plugin_fixploidy + owner: iuc + revisions: + - '365325116147' + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: bcftools_stats + owner: iuc + revisions: + - b17394940c7a + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcf2tsv + owner: devteam + revisions: + - 285060661b45 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcfhethom + owner: devteam + revisions: + - 8254e0fe7358 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: snpeff_sars_cov_2 + owner: iuc + revisions: + - 2a3a00c1fa0a + tool_panel_section_id: virology + tool_panel_section_label: Virology